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Cardoso AL, Venturelli NB, da Cruz I, de Sá Patroni FM, de Moraes D, de Oliveira RA, Benavente R, Martins C. Meiotic behavior, transmission and active genes of B chromosomes in the cichlid Astatotilapia latifasciata: new clues about nature, evolution and maintenance of accessory elements. Mol Genet Genomics 2022; 297:1151-1167. [PMID: 35704117 DOI: 10.1007/s00438-022-01911-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 05/24/2022] [Indexed: 12/23/2022]
Abstract
Supernumerary B chromosomes (Bs) are dispensable genetic elements widespread in eukaryotes and are poorly understood mainly in relation to mechanisms of maintenance and transmission. The cichlid Astatotilapia latifasciata can harbor Bs in a range of 0 (named B -) and 1-2 (named B +). The B in A. latifasciata is rich in several classes of repetitive DNA sequences, contains protein coding genes, and affects hosts in diverse ways, including sex-biased effects. To advance in the knowledge about the mechanisms of maintenance and transmission of B chromosomes in A. latifasciata, here, we studied the meiotic behavior in males and transmission rates of A. latifasciata B chromosome. We also analyzed structurally and functionally the predicted B chromosome copies of the cell cycle genes separin-like, tubb1-like and kif11-like. We identified in the meiotic structure relative to the B chromosome the presence of proteins associated with Synaptonemal Complex organization (SMC3, SYCP1 and SYCP3) and found that the B performs self-pairing. These data suggest that isochromosome formation was a step during B chromosome evolution and this element is in a stage of diversification of the two arms keeping the self-pairing behavior to protect the A chromosome complement of negative effects of recombination. Moreover, we observed no occurrence of B-drive and confirmed the presence of cell cycle genes copies in the B chromosome and their transcription in encephalon, muscle and gonads, which can indicates beneficial effects to hosts and contribute to B maintenance.
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Affiliation(s)
- Adauto Lima Cardoso
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil
| | - Natália Bortholazzi Venturelli
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil
| | - Irene da Cruz
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Fábio Malta de Sá Patroni
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil
| | - Diogo de Moraes
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil
| | - Rogério Antonio de Oliveira
- Department of Biostatistics, Plant Biology, Parasitology and Zoology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, Brazil
| | - Ricardo Benavente
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, 97074, Würzburg, Germany
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, Sao Paulo State University, UNESP, Botucatu, SP, 18618-689, Brazil.
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Kocher TD, Behrens KA, Conte MA, Aibara M, Mrosso HDJ, Green ECJ, Kidd MR, Nikaido M, Koblmüller S. New Sex Chromosomes in Lake Victoria Cichlid Fishes (Cichlidae: Haplochromini). Genes (Basel) 2022; 13:804. [PMID: 35627189 PMCID: PMC9141883 DOI: 10.3390/genes13050804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/19/2022] Open
Abstract
African cichlid fishes harbor an extraordinary diversity of sex-chromosome systems. Within just one lineage, the tribe Haplochromini, at least 6 unique sex-chromosome systems have been identified. Here we focus on characterizing sex chromosomes in cichlids from the Lake Victoria basin. In Haplochromis chilotes, we identified a new ZW system associated with the white blotch color pattern, which shows substantial sequence differentiation over most of LG16, and is likely to be present in related species. In Haplochromis sauvagei, we found a coding polymorphism in amh that may be responsible for an XY system on LG23. In Pundamilia nyererei, we identified a feminizing effect of B chromosomes together with XY- and ZW-patterned differentiation on LG23. In Haplochromis latifasciatus, we identified a duplication of amh that may be present in other species of the Lake Victoria superflock. We further characterized the LG5-14 XY system in Astatotilapia burtoni and identified the oldest stratum on LG14. This species also showed ZW differentiation on LG2. Finally, we characterized an XY system on LG7 in Astatoreochromis alluaudi. This report brings the number of distinct sex-chromosome systems in haplochromine cichlids to at least 13, and highlights the dynamic evolution of sex determination and sex chromosomes in this young lineage.
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Affiliation(s)
- Thomas D. Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, USA; (K.A.B.); (M.A.C.)
| | - Kristen A. Behrens
- Department of Biology, University of Maryland, College Park, MD 20742, USA; (K.A.B.); (M.A.C.)
| | - Matthew A. Conte
- Department of Biology, University of Maryland, College Park, MD 20742, USA; (K.A.B.); (M.A.C.)
| | - Mitsuto Aibara
- Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan; (M.A.); (M.N.)
| | - Hillary D. J. Mrosso
- Mwanza Fisheries Research Center, Tanzania Fisheries Research Institute (TAFIRI), Mwanza P.O. Box 475, Tanzania;
| | - Elizabeth C. J. Green
- Department of Biology and Chemistry, Texas A&M International University, Laredo, TX 78041, USA; (E.C.J.G.); (M.R.K.)
| | - Michael R. Kidd
- Department of Biology and Chemistry, Texas A&M International University, Laredo, TX 78041, USA; (E.C.J.G.); (M.R.K.)
| | - Masato Nikaido
- Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan; (M.A.); (M.N.)
| | - Stephan Koblmüller
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria;
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3
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Nascimento-Oliveira JI, Fantinatti BEA, Wolf IR, Cardoso AL, Ramos E, Rieder N, de Oliveira R, Martins C. Differential expression of miRNAs in the presence of B chromosome in the cichlid fish Astatotilapia latifasciata. BMC Genomics 2021; 22:344. [PMID: 33980143 PMCID: PMC8117508 DOI: 10.1186/s12864-021-07651-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND B chromosomes (Bs) are extra elements observed in diverse eukaryotes, including animals, plants and fungi. Although Bs were first identified a century ago and have been studied in hundreds of species, their biology is still enigmatic. Recent advances in omics and big data technologies are revolutionizing the B biology field. These advances allow analyses of DNA, RNA, proteins and the construction of interactive networks for understanding the B composition and behavior in the cell. Several genes have been detected on the B chromosomes, although the interaction of B sequences and the normal genome remains poorly understood. RESULTS We identified 727 miRNA precursors in the A. latifasciata genome, 66% which were novel predicted sequences that had not been identified before. We were able to report the A. latifasciata-specific miRNAs and common miRNAs identified in other fish species. For the samples carrying the B chromosome (B+), we identified 104 differentially expressed (DE) miRNAs that are down or upregulated compared to samples without B chromosome (B-) (p < 0.05). These miRNAs share common targets in the brain, muscle and gonads. These targets were used to construct a protein-protein-miRNA network showing the high interaction between the targets of differentially expressed miRNAs in the B+ chromosome samples. Among the DE-miRNA targets there are protein-coding genes reported for the B chromosome that are present in the protein-protein-miRNA network. Additionally, Gene Ontology (GO) terms related to nuclear matrix organization and response to stimulus are exclusive to DE miRNA targets of B+ samples. CONCLUSIONS This study is the first to report the connection of B chromosomes and miRNAs in a vertebrate species. We observed that the B chromosome impacts the miRNAs expression in several tissues and these miRNAs target several mRNAs involved with important biological processes.
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Affiliation(s)
- Jordana Inácio Nascimento-Oliveira
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | | | - Ivan Rodrigo Wolf
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Adauto Lima Cardoso
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Erica Ramos
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Nathalie Rieder
- Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany
| | - Rogerio de Oliveira
- Department of Biostatistics, Plant Biology, Parasitology and Zoology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Cesar Martins
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil.
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Abstract
Chromosome size and morphology vary within and among species, but little is known about the proximate or ultimate causes of these differences. Cichlid fish species in the tribe Oreochromini share an unusual giant chromosome that is ∼3 times longer than the other chromosomes. This giant chromosome functions as a sex chromosome in some of these species. We test two hypotheses of how this giant sex chromosome may have evolved. The first hypothesis proposes that it evolved by accumulating repetitive elements as recombination was reduced around a dominant sex determination locus, as suggested by canonical models of sex chromosome evolution. An alternative hypothesis is that the giant sex chromosome originated via the fusion of an autosome with a highly repetitive B chromosome, one of which carried a sex determination locus. We test these hypotheses using comparative analysis of chromosome-scale cichlid and teleost genomes. We find that the giant sex chromosome consists of three distinct regions based on patterns of recombination, gene and transposable element content, and synteny to the ancestral autosome. The WZ sex determination locus encompasses the last ∼105 Mb of the 134-Mb giant chromosome. The last 47 Mb of the giant chromosome shares no obvious homology to any ancestral chromosome. Comparisons across 69 teleost genomes reveal that the giant sex chromosome contains unparalleled amounts of endogenous retroviral elements, immunoglobulin genes, and long noncoding RNAs. The results favor the B chromosome fusion hypothesis for the origin of the giant chromosome.
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Affiliation(s)
- Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Frances E Clark
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Reade B Roberts
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Luohao Xu
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
| | - Qi Zhou
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, USA
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5
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Bednářová M, Karafiátová M, Hřibová E, Bartoš J. B Chromosomes in Genus Sorghum (Poaceae). PLANTS (BASEL, SWITZERLAND) 2021; 10:505. [PMID: 33803087 PMCID: PMC8001295 DOI: 10.3390/plants10030505] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 12/30/2022]
Abstract
B chromosomes (Bs) are supernumerary dispensable genomic elements that have been reported in several thousand eukaryotic species. Since their discovery, Bs have been subjected to countless studies aiming at the clarification of their origin, composition, and influence on the carriers. Despite these efforts, we still have very limited knowledge of the processes that led to the emergence of Bs, the mechanisms of their transmission, and the effects of Bs on the hosts. In the last decade, sophisticated molecular methods, including next-generation sequencing, have provided powerful tool to help answer some of these questions, but not many species have received much attention yet. In this review, we summarize the currently available information about Bs in the genus Sorghum, which has so far been on the periphery of scientific interest. We present an overview of the occurrence and characteristics of Bs in various Sorghum species, discuss the possible mechanisms involved in their maintenance and elimination, and outline hypotheses of the origin of Bs in this genus.
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Affiliation(s)
| | | | | | - Jan Bartoš
- Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 31, 779 00 Olomouc, Czech Republic; (M.B.); (M.K.); (E.H.)
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6
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Martins C, Jehangir M. A genomic glimpse of B chromosomes in cichlids. Genes Genomics 2021; 43:199-208. [PMID: 33547625 DOI: 10.1007/s13258-021-01049-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 01/25/2023]
Abstract
BACKGROUND B chromosomes (Bs) are extra karyotype elements in addition to A chromosomes and are found in all major eukaryotic taxa. Among hundreds of investigated species, cichlid fishes have emerged as an interesting group of model and have contributed to unravel the complex biology of B chromosome. OBJECTIVE We review the current state of knowledge on B chromosome investigation in cichlid fish and discuss the recent genomic advances over gene and sequences hunting on Bs and their impact on the current concept of B chromosomes. RESULTS The Bs of cichlids have been under the subject of classical cytogenetics and high scale DNA, RNA and epigenetics analysis and a list of B chromosome genes and functional sequences has been generated. B chromosomes of cichlids are restricted to females in some species and are enriched with genes, relics of genes, transposable elements and sequences transcribing for many significant biological functions. Diverse potentially functional sequences have been described in the B chromosome of cichlids and could influence important biological characteristics as well seems to affect transcription and epigenetic modifications of the whole genome. CONCLUSION One of the most enigmatic characteristics of Bs in cichlids is their genic content related to cell cycle and chromosome structure, and their influence over sex rates. The relationship of Bs with cell cycle and sex determination looks like to be connected with the drive of the Bs during cell divisions.
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Affiliation(s)
- Cesar Martins
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil.
| | - Maryam Jehangir
- Department of Structural and Functional Biology, Institute of Biosciences at Botucatu, São Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
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7
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Nascimento CND, Troy WP, Alves JCP, Carvalho ML, Oliveira C, Foresti F. Molecular cytogenetic analyses reveal extensive chromosomal rearrangements and novel B chromosomes in Moenkhausia (Teleostei, Characidae). Genet Mol Biol 2020; 43:e20200027. [PMID: 33156889 PMCID: PMC7649911 DOI: 10.1590/1678-4685-gmb-2020-0027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 09/01/2020] [Indexed: 11/30/2022] Open
Abstract
The cytogenetic characteristics of five fish species of the Moenkhausia are described, based on the analysis of specimens collected in different headwater. All the species analyzed presented 2n=50 chromosomes. The C-banding revealed a similar distribution pattern of heterochromatic blocks in all the species, except Moenkhausia nigromarginata. The 5S rDNA sites were distributed on multiple chromosome pairs in all five species. Single and multiple histone H1 sites were observed in all the species, and histone H1 was shown to be co-located with the 18S rRNA gene in a single chromosome pair. The U2 snDNA gene was distributed at multiple sites in all the Moenkhausia species. The presence of B microchromosomes was confirmed in Moenkhausia forestii, while individuals of the three study populations of Moenkhausia oligolepis presented three morphologically distinct types of B chromosome. The chromosomal mapping of the 18S rDNA sites using the FISH technique revealed signals in the B chromosomes of M. forestii, while clusters of the H1 histone and U2 snDNA genes were found in the B chromosomes of M. forestii and M. oligolepis. The classical and molecular cytogenetic markers used in this study revealed ample variation in the Moenkhausia karyotypes, reflecting the dynamic nature of the chromosomal evolution.
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Affiliation(s)
- Cristiano Neves do Nascimento
- Universidade Estadual Paulista - UNESP, Instituto de Biociências, Departamento de Biologia Estrutural e Funcional, Botucatu, SP, Brazil
| | - Waldo Pinheiro Troy
- Universidade do Estado de Mato Grosso - UNEMAT, Departamento de Ciências Biológicas, Tangará da Serra, MT, Brazil
| | | | - Margarida Lima Carvalho
- Universidade Federal do Acre - UFAC, Centro de Ciências Biológicas e Naturais, Rio Branco, AC, Brazil
| | - Claudio Oliveira
- Universidade Estadual Paulista - UNESP, Instituto de Biociências, Departamento de Biologia Estrutural e Funcional, Botucatu, SP, Brazil
| | - Fausto Foresti
- Universidade Estadual Paulista - UNESP, Instituto de Biociências, Departamento de Biologia Estrutural e Funcional, Botucatu, SP, Brazil
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8
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Carducci F, Barucca M, Canapa A, Carotti E, Biscotti MA. Mobile Elements in Ray-Finned Fish Genomes. Life (Basel) 2020; 10:E221. [PMID: 32992841 PMCID: PMC7599744 DOI: 10.3390/life10100221] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/18/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
Ray-finned fishes (Actinopterygii) are a very diverse group of vertebrates, encompassing species adapted to live in freshwater and marine environments, from the deep sea to high mountain streams. Genome sequencing offers a genetic resource for investigating the molecular bases of this phenotypic diversity and these adaptations to various habitats. The wide range of genome sizes observed in fishes is due to the role of transposable elements (TEs), which are powerful drivers of species diversity. Analyses performed to date provide evidence that class II DNA transposons are the most abundant component in most fish genomes and that compared to other vertebrate genomes, many TE superfamilies are present in actinopterygians. Moreover, specific TEs have been reported in ray-finned fishes as a possible result of an intricate relationship between TE evolution and the environment. The data summarized here underline the biological interest in Actinopterygii as a model group to investigate the mechanisms responsible for the high biodiversity observed in this taxon.
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Affiliation(s)
| | | | | | | | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy; (F.C.); (M.B.); (A.C.); (E.C.)
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9
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Jehangir M, Ahmad SF, Cardoso AL, Ramos E, Valente GT, Martins C. De novo genome assembly of the cichlid fish Astatotilapia latifasciata reveals a higher level of genomic polymorphism and genes related to B chromosomes. Chromosoma 2019; 128:81-96. [PMID: 31115663 DOI: 10.1007/s00412-019-00707-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/27/2019] [Accepted: 05/07/2019] [Indexed: 12/15/2022]
Abstract
Supernumerary B chromosomes (Bs) are accessory elements to the regular chromosome set (As) and have been observed in a huge diversity of eukaryotic species. Although extensively investigated, the biological significance of Bs remains enigmatic. Here, we present de novo genome assemblies for the cichlid fish Astatotilapia latifasciata, a well-known model to study Bs. High coverage data with Illumina sequencing was obtained for males and females with 0B (B-), 1B, and 2B (B+) chromosomes to provide information regarding the diversity among these genomes. The draft assemblies comprised 771 Mb for the B- genome and 781 Mb for the B+ genome. Comparative analysis of the B+ and B- assemblies reveals syntenic discontinuity, duplicated blocks and several insertions, deletions, and inversions indicative of rearrangements in the B+ genome. Hundreds of transposable elements and 1546 protein coding sequences were annotated in the duplicated B+ regions. Our work contributes a list of thousands of genes harbored on the B chromosome, with functions in several biological processes, including the cell cycle.
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Affiliation(s)
- Maryam Jehangir
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | - Syed F Ahmad
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | - Adauto L Cardoso
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | - Erica Ramos
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil
| | - Guilherme T Valente
- Bioprocess and Biotechnology Department, Agronomical Science Faculty, Sao Paulo State University - UNESP, Botucatu, SP, Brazil
| | - Cesar Martins
- Department of Morphology, Institute of Bioscience at Botucatu, São Paulo State University - UNESP, Botucatu, SP, 18618-689, Brazil.
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10
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Favarato RM, Braga Ribeiro L, Ota RP, Nakayama CM, Feldberg E. Cytogenetic Characterization of Two Metynnis Species (Characiformes, Serrasalmidae) Reveals B Chromosomes Restricted to the Females. Cytogenet Genome Res 2019; 158:38-45. [DOI: 10.1159/000499954] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2018] [Indexed: 11/19/2022] Open
Abstract
Karyotypes and chromosomal characteristics with focus on B chromosomes of 2 species of the serrasalmid genus Metynnis, namely M. lippincottianus and M. maculatus, were examined using conventional (C-banding) and molecular (FISH mapping of minor and major rDNAs and Rex1, Rex3, and Rex6 retrotransposable elements) protocols. Both species possessed a diploid chromosome number of 2n = 62 and karyotypes composed of 32 metacentric + 28 submetacentric + 2 subtelocentric and 32 metacentric + 26 submetacentric + 4 subtelocentric, respectively; one small B element was found in the female genome of M. lippincottianus. C-banding revealed heterochromatin in the pericentromeric and terminal portions of all chromosomes of both species; the B chromosome was entirely heterochromatic. FISH showed 18S rDNA sites in 2 chromosome pairs in both species (pairs 19 and 22), and a large block in the B chromosome, while 5S rDNA signals were detected in the first pair of subtelocentric chromosomes in both species, moreover in M. maculatus an additional labeled pair 4 was observed. Mapping of the Rex1, Rex3, and Rex6 retrotransposable elements in the genomes of M. lippincottianus and M. maculatus indicated that they were dispersed throughout nearly all the chromosomes of the complement, except for the B chromosome of M. lippincottianus.
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11
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Cardoso AL, Fantinatti BEDA, Venturelli NB, Carmello BDO, de Oliveira RA, Martins C. Epigenetic DNA Modifications Are Correlated With B Chromosomes and Sex in the Cichlid Astatotilapia latifasciata. Front Genet 2019; 10:324. [PMID: 31031803 PMCID: PMC6474290 DOI: 10.3389/fgene.2019.00324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/22/2019] [Indexed: 12/11/2022] Open
Abstract
Supernumerary B chromosomes are dispensable elements found in several groups of eukaryotes, and their impacts in host organisms are not clear. The cichlid fish Astatotilapia latifasciata presents one or two large metacentric B chromosomes. These elements affect the transcription of several classes of RNAs. Here, we evaluated the epigenetic DNA modification status of B chromosomes using immunocytogenetics and assessed the impact of B chromosome presence on the global contents of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) and the molecular mechanisms underlying these variations. We found that the B chromosome of A. latifasciata has an active pattern of DNA epimarks, and its presence promotes the loss of 5mC in gonads of females with B chromosome (FB+) and promotes the loss of 5hmC in the muscle of males with the B element (MB+). Based on the transcriptional quantification of DNA modification genes (dnmt, tet, and tdg) and their candidate regulators (idh genes, microRNAs, and long non-coding RNAs) and on RNA-protein interaction prediction, we suggest the occurrence of passive demethylation in gonads of FB+ and 5hmC loss by Tet inhibition or by 5hmC oxidation in MB+ muscle. We suggest that these results can also explain the previously reported variations in the transcription levels of several classes of RNA depending on B chromosome presence. The DNA modifications detected here are also influenced by sex. Although the correlation between B chromosomes and sex has been previously reported, it remains unexplained. The B chromosome of A. latifasciata seems to be active and impacts cell physiology in a very complex way, including at the epigenetic level.
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Affiliation(s)
- Adauto Lima Cardoso
- Integrative Genomics Laboratory, Department of Morphology, Institute of Biosciences, São Paulo State University - Universidade Estadual Paulista, Botucatu, Brazil
| | - Bruno Evaristo de Almeida Fantinatti
- Integrative Genomics Laboratory, Department of Morphology, Institute of Biosciences, São Paulo State University - Universidade Estadual Paulista, Botucatu, Brazil
| | - Natália Bortholazzi Venturelli
- Integrative Genomics Laboratory, Department of Morphology, Institute of Biosciences, São Paulo State University - Universidade Estadual Paulista, Botucatu, Brazil
| | - Bianca de Oliveira Carmello
- Integrative Genomics Laboratory, Department of Morphology, Institute of Biosciences, São Paulo State University - Universidade Estadual Paulista, Botucatu, Brazil
| | - Rogério Antonio de Oliveira
- Department of Biostatistics, Institute of Biosciences, São Paulo State University - Universidade Estadual Paulista, Botucatu, Brazil
| | - Cesar Martins
- Integrative Genomics Laboratory, Department of Morphology, Institute of Biosciences, São Paulo State University - Universidade Estadual Paulista, Botucatu, Brazil
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12
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Carducci F, Barucca M, Canapa A, Biscotti MA. Rex Retroelements and Teleost Genomes: An Overview. Int J Mol Sci 2018; 19:ijms19113653. [PMID: 30463278 PMCID: PMC6274825 DOI: 10.3390/ijms19113653] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/31/2018] [Accepted: 11/16/2018] [Indexed: 01/29/2023] Open
Abstract
Repetitive DNA is an intriguing portion of the genome still not completely discovered and shows a high variability in terms of sequence, genomic organization, and evolutionary mode. On the basis of the genomic organization, it includes satellite DNAs, which are organized as long arrays of head-to-tail linked repeats, and transposable elements, which are dispersed throughout the genome. These repeated elements represent a considerable fraction of vertebrate genomes contributing significantly in species evolution. In this review, we focus our attention on Rex1, Rex3 and Rex6, three elements specific of teleost genomes. We report an overview of data available on these retroelements highlighting their significative impact in chromatin and heterochromatin organization, in the differentiation of sex chromosomes, in the formation of supernumerary chromosomes, and in karyotype evolution in teleosts.
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Affiliation(s)
- Federica Carducci
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Marco Barucca
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Adriana Canapa
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy.
| | - Maria Assunta Biscotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, 60131 Ancona, Italy.
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13
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Komissarov A, Vij S, Yurchenko A, Trifonov V, Thevasagayam N, Saju J, Sridatta PSR, Purushothaman K, Graphodatsky A, Orbán L, Kuznetsova I. B Chromosomes of the Asian Seabass ( Lates calcarifer) Contribute to Genome Variations at the Level of Individuals and Populations. Genes (Basel) 2018; 9:E464. [PMID: 30241368 PMCID: PMC6211105 DOI: 10.3390/genes9100464] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 09/06/2018] [Accepted: 09/12/2018] [Indexed: 12/01/2022] Open
Abstract
The Asian seabass (Lates calcarifer) is a bony fish from the Latidae family, which is widely distributed in the tropical Indo-West Pacific region. The karyotype of the Asian seabass contains 24 pairs of A chromosomes and a variable number of AT- and GC-rich B chromosomes (Bchrs or Bs). Dot-like shaped and nucleolus-associated AT-rich Bs were microdissected and sequenced earlier. Here we analyzed DNA fragments from Bs to determine their repeat and gene contents using the Asian seabass genome as a reference. Fragments of 75 genes, including an 18S rRNA gene, were found in the Bs; repeats represented 2% of the Bchr assembly. The 18S rDNA of the standard genome and Bs were similar and enriched with fragments of transposable elements. A higher nuclei DNA content in the male gonad and somatic tissue, compared to the female gonad, was demonstrated by flow cytometry. This variation in DNA content could be associated with the intra-individual variation in the number of Bs. A comparison between the copy number variation among the B-related fragments from whole genome resequencing data of Asian seabass individuals identified similar profiles between those from the South-East Asian/Philippines and Indian region but not the Australian ones. Our results suggest that Bs might cause variations in the genome among the individuals and populations of Asian seabass. A personalized copy number approach for segmental duplication detection offers a suitable tool for population-level analysis across specimens with low coverage genome sequencing.
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Affiliation(s)
- Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia.
| | - Shubha Vij
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
- School of Applied Science, Republic Polytechnic 9 Woodlands Avenue 9, Singapore 738964, Singapore.
| | - Andrey Yurchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia.
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Vladimir Trifonov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
- Department of Natural Science, Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Natascha Thevasagayam
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
| | - Jolly Saju
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
| | | | - Kathiresan Purushothaman
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway.
| | - Alexander Graphodatsky
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
- Department of Natural Science, Novosibirsk State University, Novosibirsk 630090, Russia.
| | - László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
- Department of Animal Sciences, Georgikon Faculty, University of Pannonia, H-8360 Keszthely, Hungary.
- Center for Comparative Genomics, Murdoch University, 6150 Murdoch, Australia.
| | - Inna Kuznetsova
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
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14
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Coan RLB, Martins C. Landscape of Transposable Elements Focusing on the B Chromosome of the Cichlid Fish Astatotilapia latifasciata. Genes (Basel) 2018; 9:genes9060269. [PMID: 29882892 PMCID: PMC6027319 DOI: 10.3390/genes9060269] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 05/16/2018] [Accepted: 05/17/2018] [Indexed: 12/26/2022] Open
Abstract
B chromosomes (Bs) are supernumerary elements found in many taxonomic groups. Most B chromosomes are rich in heterochromatin and composed of abundant repetitive sequences, especially transposable elements (TEs). B origin is generally linked to the A-chromosome complement (A). The first report of a B chromosome in African cichlids was in Astatotilapia latifasciata, which can harbor 0, 1, or 2 Bs Classical cytogenetic studies found high a TE content on this B chromosome. In this study, we aimed to understand TE composition and expression in the A. latifasciata genome and its relation to the B chromosome. We used bioinformatics analysis to explore the genomic organization of TEs and their composition on the B chromosome. The bioinformatics findings were validated by fluorescent in situ hybridization (FISH) and real-time PCR (qPCR). A. latifasciata has a TE content similar to that of other cichlid fishes and several expanded elements on its B chromosome. With RNA sequencing data (RNA-seq), we showed that all major TE classes are transcribed in the brain, muscle, and male and female gonads. An evaluation of TE transcription levels between B- and B+ individuals showed that few elements are differentially expressed between these groups and that the expanded B elements are not highly transcribed. Putative silencing mechanisms may act on the B chromosome of A. latifasciata to prevent the adverse consequences of repeat transcription and mobilization in the genome.
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Affiliation(s)
- Rafael L B Coan
- Department of Morphology, Institute of Biosciences, São Paulo State University (UNESP), 18618-689 Botucatu, SP, Brazil.
| | - Cesar Martins
- Department of Morphology, Institute of Biosciences, São Paulo State University (UNESP), 18618-689 Botucatu, SP, Brazil.
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15
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Malimpensa GC, Traldi JB, Toyama D, Henrique-Silva F, Vicari MR, Moreira-Filho O. Chromosomal Mapping of Repeat DNA in Bergiaria westermanni (Pimelodidae, Siluriformes): Localization of 45S rDNA in B Chromosomes. Cytogenet Genome Res 2018; 154:99-106. [PMID: 29635248 DOI: 10.1159/000487652] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2017] [Indexed: 12/19/2022] Open
Abstract
The occurrence of repetitive DNA in autosomes and B chromosomes of Bergiaria westermanni was examined using conventional and molecular cytogenetic techniques. This species exhibited 2n = 56 chromosomes, with intra- and interindividual variation in the number of heterochromatic B chromosomes (from 0 to 4). The 5S rDNA was localized in pairs 1 and 5, and histone probes (H1, H3, and H4) and U2 small nuclear RNA were syntenic with 5S rDNA in pair 5. Histone sequences were also located in chromosome pair 14. The (GATA)n sequence was dispersed throughout the autosomes and B chromosomes, with clusters (microsatellite accumulation) in some chromosome regions. The telomeric probe revealed no signs of chromosomal rearrangements in the genome of B. westermanni. The 45S rDNA sites were detected in the terminal region of pair 27; these sites corresponded to a GC-rich heterochromatin block. In addition, 3 of the 4 B chromosomes also contained 45S rDNA copies. Silver nitrate staining in interphase nuclei provided indirect evidence of the expression of these rRNA genes in B chromosomes, indicating the probable origin of these elements. This report shows plasticity in the chromosomal localization of repeat DNA in B. westermanni and features a discussion of genomic diversification.
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Affiliation(s)
- Geovana C Malimpensa
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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16
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Perazzo GX, Noleto RB, Vicari MR, Gava A, Cestari MM. B chromosome polymorphism in South American cichlid. NEOTROPICAL BIODIVERSITY 2018. [DOI: 10.1080/23766808.2018.1429164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
| | - Rafael Bueno Noleto
- Department of Biology, State University of Paraná, União da Vitória, Paraná, Brazil
| | - Marcelo Ricardo Vicari
- Department of Structural, Molecular and Genetical Biology, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Adriana Gava
- Biological Sciences Institute, Federal University of Rio Grande, Rio Grande, Brazil
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17
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Transcription of a B chromosome CAP-G pseudogene does not influence normal Condensin Complex genes in a grasshopper. Sci Rep 2017; 7:17650. [PMID: 29247237 PMCID: PMC5732253 DOI: 10.1038/s41598-017-15894-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/02/2017] [Indexed: 11/08/2022] Open
Abstract
Parasitic B chromosomes invade and persist in natural populations through several mechanisms for transmission advantage (drive). They may contain gene-derived sequences which, in some cases, are actively transcribed. A further interesting question is whether B-derived transcripts become functional products. In the grasshopper Eyprepocnemis plorans, one of the gene-derived sequences located on the B chromosome shows homology with the gene coding for the CAP-G subunit of condensin I. We show here, by means of fluorescent in situ hybridization coupled with tyramide signal amplification (FISH-TSA), that this gene is located in the distal region of the B24 chromosome variant. The DNA sequence located in the B chromosome is a pseudogenic version of the CAP-G gene (B-CAP-G). In two Spanish populations, we found active transcription of B-CAP-G, but it did not influence the expression of CAP-D2 and CAP-D3 genes coding for corresponding condensin I and II subunits, respectively. Our results indicate that the transcriptional regulation of the B-CAP-G pseudogene is uncoupled from the standard regulation of the genes that constitute the condensin complex, and suggest that some of the B chromosome known effects may be related with its gene content and transcriptional activity, thus opening new exciting avenues for research.
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18
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Carvalho PC, de Oliveira EA, Bertollo LAC, Yano CF, Oliveira C, Decru E, Jegede OI, Hatanaka T, Liehr T, Al-Rikabi ABH, Cioffi MDB. First Chromosomal Analysis in Hepsetidae (Actinopterygii, Characiformes): Insights into Relationship between African and Neotropical Fish Groups. Front Genet 2017; 8:203. [PMID: 29312435 PMCID: PMC5733008 DOI: 10.3389/fgene.2017.00203] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 11/22/2017] [Indexed: 01/27/2023] Open
Abstract
Hepsetidae is a small fish family with only the genus Hepsetus, with six described species distributed throughout the South, Central and Western regions of Africa, showing a close relationship with the Alestidae and some Neotropical fish families. However, no cytogenetic information is available for both Hepsetidae and Alestidae species, thus preventing any evolutionary comparative studies at the chromosomal level. In the present study, we are providing new cytogenetic data for Hepsetus odoe, including the standard karyotype, C-banding, repetitive DNAs mapping, comparative genomic hybridization (CGH) and whole chromosome painting (WCP), providing chromosomal patterns and subsidies for comparative cytogenetics with other characiform families. Both males and females H. odoe have 2n = 58 chromosomes (10m + 28sm + 20st/a), with most of the C-band positive heterochromatin localized in the centromeric and subtelomeric regions. Only one pair of chromosomes bears proximal 5S rDNA sites in the short arms, contrasting with the 18S rDNA sequences which are located in the terminal regions of four chromosome pairs. Clear interstitial hybridization signals are evidenced for the U1 and U2 snDNA probes, but in only one and two chromosome pairs, respectively. Microsatellite motifs are widely distributed in the karyotype, with exception for the (CGG)10, (GAA)10 and (GAG)10 probes, which highlight conspicuous interstitial signals on an unique pair of chromosomes. Comparative data from conventional and molecular cytogenetics, including CGH and WCP experiments, indicate that H. odoe and some Erythrinidae species, particularly Erythrinus erythrinus, share similar chromosomal sequences suggesting some relatedness among them, although bearing genomic specificities in view of their divergent evolutionary histories.
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Affiliation(s)
- Pedro C Carvalho
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Ezequiel A de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil.,Secretaria de Estado de Educação de Mato Grosso (Seduc-MT), Cuiabá, Brazil
| | - Luiz A C Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Cassia F Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Claudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - Eva Decru
- Section Vertebrates, Ichthyology, Royal Museum for Central Africa, Tervuren, Belgium
| | - Oladele I Jegede
- Department of Fisheries and Aquaculture, Adamawa State University, Mubi, Nigeria
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | | | - Marcelo de B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
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19
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Carmello BO, Coan RLB, Cardoso AL, Ramos E, Fantinatti BEA, Marques DF, Oliveira RA, Valente GT, Martins C. The hnRNP Q-like gene is retroinserted into the B chromosomes of the cichlid fish Astatotilapia latifasciata. Chromosome Res 2017; 25:277-290. [PMID: 28776210 DOI: 10.1007/s10577-017-9561-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/12/2017] [Accepted: 07/14/2017] [Indexed: 11/27/2022]
Abstract
B chromosomes are dispensable elements observed in many eukaryotic species, including the African cichlid Astatotilapia latifasciata, which might have one or two B chromosomes. Although there have been many studies focused on the biology of these chromosomes, questions about the evolution, maintenance, and potential effects of these chromosomes remain. Here, we identified a variant form of the hnRNP Q-like gene inserted into the B chromosome of A. latifasciata that is characterized by a high copy number and intron-less structure. The absence of introns and presence of transposable elements with a reverse transcriptase domain flanking hnRNP Q-like sequences suggest that this gene was retroinserted into the B chromosome. RNA-Seq analysis did not show that the B variant retroinserted copies are transcriptionally active. However, RT-qPCR results showed variations in the canonical hnRNP Q-like copy expression levels among exons, tissues, sex, and B presence/absence. Although the patterns of transcription are not well understood, the exons of the B retrocopies were overexpressed, and a bias for female B+ expression was also observed. These results suggest that retroinsertion is an additional and important mechanism contributing to B chromosome formation. Furthermore, these findings indicate a bias towards female differential expression of B chromosome sequences, suggesting that B chromosomes and sex determination are somehow associated in cichlids.
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Affiliation(s)
- Bianca O Carmello
- Institute of Biosciences, Department of Morphology, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Rafael L B Coan
- Institute of Biosciences, Department of Morphology, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Adauto L Cardoso
- Institute of Biosciences, Department of Morphology, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Erica Ramos
- Institute of Biosciences, Department of Morphology, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Bruno E A Fantinatti
- Institute of Biosciences, Department of Morphology, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Diego F Marques
- Institute of Biosciences, Department of Morphology, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Rogério A Oliveira
- Institute of Biosciences, Department of Biostatistics, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil
| | - Guilherme T Valente
- Institute of Biosciences, Agronomic Science School, Department of Bioprocess and Biotechnology, Sao Paulo State University (UNESP), Botucatu, SP, 18610-307, Brazil
| | - Cesar Martins
- Institute of Biosciences, Department of Morphology, Sao Paulo State University (UNESP), Botucatu, SP, 18618-689, Brazil.
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20
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Rajičić M, Romanenko SA, Karamysheva TV, Blagojević J, Adnađević T, Budinski I, Bogdanov AS, Trifonov VA, Rubtsov NB, Vujošević M. The origin of B chromosomes in yellow-necked mice (Apodemus flavicollis)-Break rules but keep playing the game. PLoS One 2017; 12:e0172704. [PMID: 28329013 PMCID: PMC5362141 DOI: 10.1371/journal.pone.0172704] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 02/08/2017] [Indexed: 12/30/2022] Open
Abstract
B chromosomes (Bs) are known for more than hundred years but their origin, structure and pattern of evolution are not well understood. In the past few years new methodological approaches, involving isolation of Bs followed by whole DNA amplification, DNA probe generation, and fluorescent in situ hybridization (FISH) or the B chromosome DNA sequencing, has allowed detailed analysis of their origin and molecular structure in different species. In this study we explored the origin of Bs in the yellow-necked wood mouse, Apodemus flavicollis, using generation of microdissected DNA probes followed by FISH on metaphase chromosomes. Bs of A. flavicollis were successfully isolated and DNA was used as the template for B-specific probes for the first time. We revealed homology of DNA derived from the analyzed B chromosomes to the pericentromeric region (PR) of sex chromosomes and subtelomeric region of two pairs of small autosomes, but lower homology to the rest of the Y chromosome. Moreover, all analysed Bs had the same structure regardless of their number per individual or the great geographic distance between examined populations from the Balkan Peninsula (Serbia) and Eastern Europe (south region of Russia and central Belarus). Therefore, it was suggested that B chromosomes in A. flavicollis have a unique common origin from the PR of sex chromosomes, and/or similar evolutionary pattern.
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Affiliation(s)
- M Rajičić
- Department for Genetic Research, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade Serbia
| | - S A Romanenko
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk Russia
| | - T V Karamysheva
- Institute of Cytology and Genetics, SB RAS, Novosibirsk Russia
| | - J Blagojević
- Department for Genetic Research, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade Serbia
| | - T Adnađević
- Department for Genetic Research, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade Serbia
| | - I Budinski
- Department for Genetic Research, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade Serbia
| | - A S Bogdanov
- Koltzov Institute of Developmental Biology, RAS, Moscow Russia
| | - V A Trifonov
- Institute of Molecular and Cellular Biology, SB RAS, Novosibirsk Russia
| | - N B Rubtsov
- Institute of Cytology and Genetics, SB RAS, Novosibirsk Russia
| | - M Vujošević
- Department for Genetic Research, Institute for Biological Research "Siniša Stanković", University of Belgrade, Belgrade Serbia
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21
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Clark FE, Conte MA, Ferreira-Bravo IA, Poletto AB, Martins C, Kocher TD. Dynamic Sequence Evolution of a Sex-Associated B Chromosome in Lake Malawi Cichlid Fish. J Hered 2016; 108:53-62. [PMID: 27630131 DOI: 10.1093/jhered/esw059] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 08/26/2016] [Indexed: 12/16/2022] Open
Abstract
B chromosomes are extra chromosomes found in many species of plants, animals, and fungi. B chromosomes often manipulate common cellular processes to increase their frequency, sometimes to the detriment of organismal fitness. Here, we characterize B chromosomes in several species of Lake Malawi cichlid fish. Whole genome sequencing of Metriaclima zebra "Boadzulu" individuals revealed blocks of sequence with unusually high sequence coverage, indicative of increased copy number of those sequences. These regions of high sequence coverage were found only in females. SNPs unique to the high copy number sequences permitted the design of specific amplification primers. These primers amplified fragments only in Metriaclima lombardoi individuals that carried a cytologically identified B chromosome (B-carriers), indicating these extra copies are located on the B chromosome. These same primers were used to identify B-carrying individuals in additional species from Lake Malawi. Across 7 species, a total of 43 B-carriers were identified among 323 females. B-carriers were exclusively female; no B chromosomes were observed in the 317 males surveyed from these species. Quantitative analysis of the copy number variation of B-specific sequence blocks suggests that B-carriers possess a single B chromosome, consistent with previous karyotyping of M. lombardoi A single B chromosome in B-carriers is consistent with 2 potential drive mechanisms: one involving nondisjunction and preferential segregation in a mitotic division prior to the germ-line, and the other involving preferential segregation during meiosis I.
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Affiliation(s)
- Frances E Clark
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins)
| | - Matthew A Conte
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins)
| | - Irani A Ferreira-Bravo
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins)
| | - Andreia B Poletto
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins)
| | - Cesar Martins
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins)
| | - Thomas D Kocher
- From the Department of Biology, University of Maryland, College Park, Maryland 20742 (Clark, Conte, and Kocher); Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland 20742 (Ferreira-Bravo); and Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, Botucatu, SP, Brazil (Poletto and Martins).
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22
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Fantinatti BEA, Martins C. Development of chromosomal markers based on next-generation sequencing: the B chromosome of the cichlid fish Astatotilapia latifasciata as a model. BMC Genet 2016; 17:119. [PMID: 27539214 PMCID: PMC4991083 DOI: 10.1186/s12863-016-0427-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 08/14/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND B chromosomes (Bs) are additional chromosomal elements found in a wide range of eukaryotes including fungi, plants and animals. B chromosomes are still enigmatic despite being the subject of hundreds, even thousands of reports. As yet there is no comprehensive theory for the biological role of B chromsomes thus, new studies are needed. Next-generation sequencing (NGS) holds promise for investigating classical issues in chromosome biology. NGS uses a large-scale approach that is required for advancing classical cytogenetic studies. Based on 454 sequencing data of a microdissected B chromosome and Illumina whole-genome sequencing data generated for 0B, 1B and 2B animals, we developed PCR- and qPCR-based markers for the B chromosomes of the cichlid fish Astatotilapia latifasciata (that possess 0, 1 or 2 B chromosomes). RESULTS Specific PCR primers were designed to produce two amplified fragments for B-positive samples and the control fragment for B-negative samples. Thus, PCR markers detected the presence/absence of Bs but did not provide information about the number of Bs. However, quantitative PCR (qPCR) markers clearly discriminated between 1B and 2B samples. The high copy number of the marker identified in the B chromosomes was confirmed by chromosome mapping. CONCLUSIONS The analysis of chromosome polymorphisms based on a NGS approach is a powerful strategy to obtain markers that detect the presence/absence of extra chromosomes or the gain or loss of genomic blocks. Further, qPCR can also provide information regarding the relative copy number of specific DNA fragments. These methods are useful to investigate various chromosome polymorphisms, including B and sex chromosomes, as well as chromosomal duplications and deletions. NGS data provide a detailed analysis of the composition of genomic regions that are thought to be present in B chromosomes.
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Affiliation(s)
- Bruno E A Fantinatti
- Departamento de Morfologia, Instituto de Biociências, UNESP - Universidade Estadual Paulista, CEP 18618-689, Botucatu, SP, Brazil
| | - Cesar Martins
- Departamento de Morfologia, Instituto de Biociências, UNESP - Universidade Estadual Paulista, CEP 18618-689, Botucatu, SP, Brazil.
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Ramos É, Cardoso AL, Brown J, Marques DF, Fantinatti BEA, Cabral-de-Mello DC, Oliveira RA, O'Neill RJ, Martins C. The repetitive DNA element BncDNA, enriched in the B chromosome of the cichlid fish Astatotilapia latifasciata, transcribes a potentially noncoding RNA. Chromosoma 2016; 126:313-323. [PMID: 27169573 DOI: 10.1007/s00412-016-0601-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/03/2016] [Accepted: 05/03/2016] [Indexed: 12/27/2022]
Abstract
Supernumerary chromosomes have been studied in many species of eukaryotes, including the cichlid fish, Astatotilapia latifasciata. However, there are many unanswered questions about the maintenance, inheritance, and functional aspects of supernumerary chromosomes. The cichlid family has been highlighted as a model for evolutionary studies, including those that focus on mechanisms of chromosome evolution. Individuals of A. latifasciata are known to carry up to two B heterochromatic isochromosomes that are enriched in repetitive DNA and contain few intact gene sequences. We isolated and characterized a transcriptionally active repeated DNA, called B chromosome noncoding DNA (BncDNA), highly represented across all B chromosomes of A. latifasciata. BncDNA transcripts are differentially processed among six different tissues, including the production of smaller transcripts, indicating transcriptional variation may be linked to B chromosome presence and sexual phenotype. The transcript lengths and lack of similarity with known protein/gene sequences indicate BncRNA might represent a novel long noncoding RNA family (lncRNA). The potential for interaction between BncRNA and known miRNAs were computationally predicted, resulting in the identification of possible binding of this sequence in upregulated miRNAs related to the presence of B chromosomes. In conclusion, Bnc is a transcriptionally active repetitive DNA enriched in B chromosomes with potential action over B chromosome maintenance in somatic cells and meiotic drive in gametic cells.
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Affiliation(s)
- Érica Ramos
- Department of Morphology, Institute of Biosciences, Sao Paulo State University, 18618-689, Botucatu, SP, Brazil
| | - Adauto L Cardoso
- Department of Morphology, Institute of Biosciences, Sao Paulo State University, 18618-689, Botucatu, SP, Brazil
| | - Judith Brown
- Allied Health Sciences Department and Institute for Systems Genomics, University of Connecticut, 06269, Storrs, CT, USA
| | - Diego F Marques
- Department of Morphology, Institute of Biosciences, Sao Paulo State University, 18618-689, Botucatu, SP, Brazil
| | - Bruno E A Fantinatti
- Department of Morphology, Institute of Biosciences, Sao Paulo State University, 18618-689, Botucatu, SP, Brazil
| | - Diogo C Cabral-de-Mello
- Department of Biology, Institute of Biosciences, Sao Paulo State University, 13506-900, Rio Claro, SP, Brazil
| | - Rogério A Oliveira
- Department of Biostatistics, Institute of Biosciences, Sao Paulo State University, 18618-689, Botucatu, SP, Brazil
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology and Institute for Systems Genomics, University of Connecticut, 06269, Storrs, CT, USA
| | - Cesar Martins
- Department of Morphology, Institute of Biosciences, Sao Paulo State University, 18618-689, Botucatu, SP, Brazil.
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24
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Silva FAD, Carvalho NDM, Schneider CH, Terencio ML, Feldberg E, Gross MC. Comparative Cytotaxonomy of Two Species of Fish from the Genus Satanoperca Reveals the Presence of a B Chromosome. Zebrafish 2016; 13:354-9. [PMID: 27158927 DOI: 10.1089/zeb.2016.1276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The taxonomy of Satanoperca spp. is still unresolved, especially because coloring, one of the main diagnostic characters, is variable among species of this genus. Thus, the aim of this study was to elucidate the relationship between the genome and the organization of the chromosome in two Satanoperca species. Our main goal was to develop a method to better differentiate taxa and understand the evolution of Satanoperca jurupari and Satanoperca lilith karyotypes, which we analyzed with classical and molecular cytogenetics. Both species have the same diploid number (2n) of 48 and location of 5S rDNA sites on pair 5. Nonetheless, the distribution of heterochromatin and 18S rDNA sites followed a species-specific pattern. The interstitial telomeric sites were not highlighted in either species. Regardless, a single B chromosome was identified in some metaphases of S. lilith. These data show that Satanoperca species harbor chromosomal features that can be used to identify the two species of Satanoperca studied here, allowing for the use of cytogenetic markers to make taxonomic inferences within the genus.
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Affiliation(s)
- Francijara Araújo da Silva
- 1 Laboratório de Citogenômica Animal, Departamento de Genética, Instituto de Ciências Biológicas , Universidade Federal do Amazonas, Manaus, Brazil
| | - Natália Dayane Moura Carvalho
- 1 Laboratório de Citogenômica Animal, Departamento de Genética, Instituto de Ciências Biológicas , Universidade Federal do Amazonas, Manaus, Brazil
| | - Carlos Henrique Schneider
- 1 Laboratório de Citogenômica Animal, Departamento de Genética, Instituto de Ciências Biológicas , Universidade Federal do Amazonas, Manaus, Brazil
| | - Maria Leandra Terencio
- 2 Instituto de Ciências da Vida e da Natureza, Departamento de Medicina, Universidade Federal de Integração Latino Americana , Foz do Iguaçu, Brazil
| | - Eliana Feldberg
- 3 Laboratório de Genética Animal, Instituto Nacional de Pesquisas da Amazônia , Manaus, Brazil
| | - Maria Claudia Gross
- 2 Instituto de Ciências da Vida e da Natureza, Departamento de Medicina, Universidade Federal de Integração Latino Americana , Foz do Iguaçu, Brazil
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25
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Integrated cytogenetics and genomics analysis of transposable elements in the Nile tilapia, Oreochromis niloticus. Mol Genet Genomics 2016; 291:1219-25. [PMID: 26860923 DOI: 10.1007/s00438-016-1176-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 01/21/2016] [Indexed: 10/22/2022]
Abstract
Integration of cytogenetics and genomics has become essential to a better view of architecture and function of genomes. Although the advances on genomic sequencing have contributed to study genes and genomes, the repetitive DNA fraction of the genome is still enigmatic and poorly understood. Among repeated DNAs, transposable elements (TEs) are major components of eukaryotic chromatin and their investigation has been hindered even after the availability of whole sequenced genomes. The cytogenetic mapping of TEs in chromosomes has proved to be of high value to integrate information from the micro level of nucleotide sequence to a cytological view of chromosomes. Different TEs have been cytogenetically mapped in cichlids; however, neither details about their genomic arrangement nor appropriated copy number are well defined by these approaches. The current study integrates TEs distribution in Nile tilapia Oreochromis niloticus genome based on cytogenetic and genomics/bioinformatics approach. The results showed that some elements are not randomly distributed and that some are genomic dependent on each other. Moreover, we found extensive overlap between genomics and cytogenetics data and that tandem duplication may be the major mechanism responsible for the genomic dynamics of TEs here analyzed. This paper provides insights in the genomic organization of TEs under an integrated view based on cytogenetics and genomics.
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26
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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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27
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Ventura K, O’Brien PCM, do Nascimento Moreira C, Yonenaga-Yassuda Y, Ferguson-Smith MA. On the Origin and Evolution of the Extant System of B Chromosomes in Oryzomyini Radiation (Rodentia, Sigmodontinae). PLoS One 2015; 10:e0136663. [PMID: 26305702 PMCID: PMC4549248 DOI: 10.1371/journal.pone.0136663] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 08/06/2015] [Indexed: 01/21/2023] Open
Abstract
Heterogeneous supernumerary chromosomes (Bs) are recognized in the oryzomyines Holochilus brasiliensis, Nectomys rattus, N. squamipes, Oligoryzomys flavescens and Sooretamys angouya, representing about 10% of all known B-containing rodent species. They provide an outstanding model for understanding the origin, evolution and diversity of Bs in a phylogenetic context. Therefore, whole chromosome-specific probes were generated from flow-sorted Holochilus brasiliensis (HBR) autosomes 11 and 25+26 and chromosomes X, Y and Bs. Hybridizations were performed on male metaphases of 15 Oryzomyini species of which 3 are B-containing species. The results reveal that among the species sampled, 12 of them, belonging to a monophyletic Oryzomiyini subclade, are positive for an anonymous Oryzomyini shared heterochromatic region (OSHR) on both sex chromosomes. The OSHR is also present on Bs of Holochilus brasiliensis, Nectomys rattus and N. squamipes but not on Bs of O. flavescens and S. angouya. Two distinct additional OSHR/autosome associations are observed on S. angouya. The three species that are OSHR negative belong to an outgroup. Molecular dating suggests that the OSHR originated between 7.8 and 3 Mya on ancestral sex chromosomes. A tentative explanation for the OSHR-positive nature of B regions in three species could be that transposable elements (TEs) from this specific sex chromosome region may have invaded existing B chromosomes. The presence of the OSHR on entire Xp and Yp adjacent to interstitial telomeric sequences at pericentromeric positions, as observed in Drymoreomys albimaculatus, show a similar organization as on B chromosomes in Nectomys squamipes. The diversity of the Oryzomyini Bs in number, size, morphology and genetic content may be explained by the independent origin of B chromosomes in different subgroups of species, with Bs in Holochilus brasiliensis, Nectomys squamipes and N. rattus sharing the OSHR with sex chromosomes, and those in Oligoryzomys flavescens and Sooretamys angouya lacking OSHR in Bs. The species-specific pattern of Bs is probably a consequence of their independent evolutionary origin.
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Affiliation(s)
- Karen Ventura
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
- Instituto de Recursos Naturais - Universidade Federal de Itajubá, Itajubá, Minas Gerais, Brazil
| | - Patricia Caroline Mary O’Brien
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Camila do Nascimento Moreira
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Yatiyo Yonenaga-Yassuda
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Malcolm Andrew Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
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28
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Sampaio TR, Gouveia JG, da Silva CRM, Dias AL, da Rosa R. Molecular Analysis of the B Microchromosome in Steindachnerina insculpta (Characiformes: Curimatidae) by Microdissection. Cytogenet Genome Res 2015; 146:51-7. [PMID: 25999244 DOI: 10.1159/000381932] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Indexed: 11/19/2022] Open
Abstract
B chromosomes are additional elements to standard karyotypes observed in different species of fishes, especially in Curimatidae. However, despite studies demonstrating the occurrence of Bs, little is known about their origin and evolution. To better understand the genomic composition and evolutionary processes involving B chromosomes, microdissection of B microchromosomes in Steindachnerina insculpta was conducted. Chromosome painting revealed the totally hybridized B and markings on A chromosomes both in S. in sculpta and in Cyphocharax spilotus, demonstrating a strong homology between these different species. In specimens of C. modestus, which do not have Bs, the signals were observed on A chromosomes. Cloning and sequencing of some B fragments revealed that the B microchromosome in S. insculpta is composed of repetitive elements, homologous to the DIRS-4 LTR retrotransposon of Xenopus (Silurana) tropicalis. FISH with clone pSi48 with the DIRS-4 retroelement revealed signals on all A chromosomes in the 2 species and also on the B, suggesting the insertion of repetitive elements in these species.
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Affiliation(s)
- Tatiane R Sampaio
- Departamento de Biologia Geral, CCB, Universidade Estadual de Londrina (UEL), Londrina, Brazil
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29
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Makunin AI, Dementyeva PV, Graphodatsky AS, Volobouev VT, Kukekova AV, Trifonov VA. Genes on B chromosomes of vertebrates. Mol Cytogenet 2014; 7:99. [PMID: 25538793 PMCID: PMC4274688 DOI: 10.1186/s13039-014-0099-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/05/2014] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND There is a growing body of evidence that B chromosomes, once regarded as totally heterochromatic and genetically inert, harbor multiple segmental duplications containing clusters of ribosomal RNA genes, processed pseudogenes and protein-coding genes. Application of novel molecular approaches further supports complex composition and possible phenotypic effects of B chromosomes. RESULTS Here we review recent findings of gene-carrying genomic segments on B chromosomes from different vertebrate groups. We demonstrate that the genetic content of B chromosomes is highly heterogeneous and some B chromosomes contain multiple large duplications derived from various chromosomes of the standard karyotype. Although B chromosomes seem to be mostly homologous to each other within a species, their genetic content differs between species. There are indications that some genomic regions are more likely to be located on B chromosomes. CONCLUSIONS The discovery of multiple autosomal genes on B chromosomes opens a new discussion about their possible effects ranging from sex determination to fitness and adaptation, their complex interactions with host genome and role in evolution.
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Affiliation(s)
- Alexey I Makunin
- />Institute of Molecular and Cellular Biology SВ RAS, Novosibirsk, 630090 Russia
- />Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Polina V Dementyeva
- />Institute of Molecular and Cellular Biology SВ RAS, Novosibirsk, 630090 Russia
| | - Alexander S Graphodatsky
- />Institute of Molecular and Cellular Biology SВ RAS, Novosibirsk, 630090 Russia
- />Novosibirsk State University, Novosibirsk, Russia
| | - Vitaly T Volobouev
- />Museum National d’Histoire Naturelle, Origine, Structure et Evolution de la Biodiversite, Paris, France
| | - Anna V Kukekova
- />Department of Animal Sciences, The University of Illinois at Urbana-Champaign, Champaign, USA
| | - Vladimir A Trifonov
- />Institute of Molecular and Cellular Biology SВ RAS, Novosibirsk, 630090 Russia
- />Novosibirsk State University, Novosibirsk, Russia
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30
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Pansonato-Alves JC, Serrano ÉA, Utsunomia R, Camacho JPM, da Costa Silva GJ, Vicari MR, Artoni RF, Oliveira C, Foresti F. Single origin of sex chromosomes and multiple origins of B chromosomes in fish genus Characidium. PLoS One 2014; 9:e107169. [PMID: 25226580 PMCID: PMC4165761 DOI: 10.1371/journal.pone.0107169] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/08/2014] [Indexed: 12/17/2022] Open
Abstract
Chromosome painting with DNA probes obtained from supernumerary (B) and sex chromosomes in three species of fish genus Characidium (C. gomesi, C. pterostictum and C. oiticicai) showed a close resemblance in repetitive DNA content between B and sex chromosomes in C. gomesi and C. pterostictum. This suggests an intraspecific origin for B chromosomes in these two species, probably deriving from sex chromosomes. In C. oiticicai, however, a DNA probe obtained from its B chromosome hybridized with the B but not with the A chromosomes, suggesting that the B chromosome in this species could have arisen interspecifically, although this hypothesis needs further investigation. A molecular phylogenetic analysis performed on nine Characidium species, with two mtDNA genes, showed that the presence of heteromorphic sex chromosomes in these species is a derived condition, and that their origin could have been unique, a conclusion also supported by interspecific chromosome painting with a CgW probe derived from the W chromosome in C. gomesi. Summing up, our results indicate that whereas heteromorphic sex chromosomes in the genus Characidium appear to have had a common and unique origin, B chromosomes may have had independent origins in different species. Our results also show that molecular phylogenetic analysis is an excellent complement for cytogenetic studies by unveiling the direction of evolutionary chromosome changes.
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Affiliation(s)
- José Carlos Pansonato-Alves
- Universidade Estadual Paulista (UNESP), Instituto de Biociências/IB, Departamento de Morfologia, Botucatu, São Paulo, Brazil
- * E-mail:
| | - Érica Alves Serrano
- Universidade Estadual Paulista (UNESP), Instituto de Biociências/IB, Departamento de Morfologia, Botucatu, São Paulo, Brazil
| | - Ricardo Utsunomia
- Universidade Estadual Paulista (UNESP), Instituto de Biociências/IB, Departamento de Morfologia, Botucatu, São Paulo, Brazil
| | | | - Guilherme José da Costa Silva
- Universidade Estadual Paulista (UNESP), Instituto de Biociências/IB, Departamento de Morfologia, Botucatu, São Paulo, Brazil
| | - Marcelo Ricardo Vicari
- Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, Paraná, Brazil
| | - Roberto Ferreira Artoni
- Universidade Estadual de Ponta Grossa, Departamento de Biologia Estrutural, Molecular e Genética, Ponta Grossa, Paraná, Brazil
| | - Cláudio Oliveira
- Universidade Estadual Paulista (UNESP), Instituto de Biociências/IB, Departamento de Morfologia, Botucatu, São Paulo, Brazil
| | - Fausto Foresti
- Universidade Estadual Paulista (UNESP), Instituto de Biociências/IB, Departamento de Morfologia, Botucatu, São Paulo, Brazil
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31
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Valente GT, Conte MA, Fantinatti BE, Cabral-de-Mello DC, Carvalho RF, Vicari MR, Kocher TD, Martins C. Origin and Evolution of B Chromosomes in the Cichlid Fish Astatotilapia latifasciata Based on Integrated Genomic Analyses. Mol Biol Evol 2014; 31:2061-72. [DOI: 10.1093/molbev/msu148] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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32
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Silva DMZDA, Pansonato-Alves JC, Utsunomia R, Araya-Jaime C, Ruiz-Ruano FJ, Daniel SN, Hashimoto DT, Oliveira C, Camacho JPM, Porto-Foresti F, Foresti F. Delimiting the origin of a B chromosome by FISH mapping, chromosome painting and DNA sequence analysis in Astyanax paranae (Teleostei, Characiformes). PLoS One 2014; 9:e94896. [PMID: 24736529 PMCID: PMC3988084 DOI: 10.1371/journal.pone.0094896] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 03/19/2014] [Indexed: 12/19/2022] Open
Abstract
Supernumerary (B) chromosomes have been shown to contain a wide variety of repetitive sequences. For this reason, fluorescent in situ hybridisation (FISH) is a useful tool for ascertaining the origin of these genomic elements, especially when combined with painting from microdissected B chromosomes. In order to investigate the origin of B chromosomes in the fish species Astyanax paranae, these two approaches were used along with PCR amplification of specific DNA sequences obtained from the B chromosomes and its comparison with those residing in the A chromosomes. Remarkably, chromosome painting with the one-arm metacentric B chromosome probe showed hybridization signals on entire B chromosome, while FISH mapping revealed the presence of H1 histone and 18S rDNA genes symmetrically placed in both arms of the B chromosome. These results support the hypothesis that the B chromosome of A. paranae is an isochromosome. Additionally, the chromosome pairs Nos. 2 or 23 are considered the possible B chromosome ancestors since both contain syntenic H1 and 18S rRNA sequences. The analysis of DNA sequence fragments of the histone and rRNA genes obtained from the microdissected B chromosomes showed high similarity with those obtained from 0B individuals, which supports the intraspecific origin of B chromosomes in A. paranae. Finally, the population hereby analysed showed a female-biased B chromosome presence suggesting that B chromosomes in this species could influence sex determinism.
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Affiliation(s)
- Duílio M. Z. de A. Silva
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
| | - José Carlos Pansonato-Alves
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
| | - Ricardo Utsunomia
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
| | - Cristian Araya-Jaime
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
| | | | - Sandro Natal Daniel
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Campus de Bauru, Bauru, São Paulo, Brazil
| | - Diogo Teruo Hashimoto
- CAUNESP, Universidade Estadual Paulista, Campus Jaboticabal, Jaboticabal, São Paulo, Brazil
| | - Cláudio Oliveira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
| | | | - Fábio Porto-Foresti
- Departamento de Ciências Biológicas, Faculdade de Ciências, Universidade Estadual Paulista, Campus de Bauru, Bauru, São Paulo, Brazil
| | - Fausto Foresti
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Distrito de Rubião Junior, Botucatu, São Paulo, Brazil
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33
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Splendore de Borba R, Lourenço da Silva E, Parise-Maltempi PP. Chromosome mapping of retrotransposable elements Rex1 and Rex3 in Leporinus Spix, 1829 species (Characiformes: Anostomidae) and its relationships among heterochromatic segments and W sex chromosome. Mob Genet Elements 2013; 3:e27460. [PMID: 24404417 DOI: 10.4161/mge.27460] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 11/28/2013] [Accepted: 12/08/2013] [Indexed: 01/21/2023] Open
Abstract
The family Anostomidae is an interesting model for studies of repetitive elements, mainly because of the presence of high numbers of heterochromatic segments related to a peculiar system of female heterogamety, which is restricted to a few species of Leporinus genus. Thus, cytogenetic mapping of the retrotransposable elements Rex1, Rex3, and Rex6 was performed in six Leporinus species, to elucidate the genomic organization of this genus. The sequencing of the Rex1 and Rex3 elements detected different base pair compositions in these elements among species, whereas the Rex6 element was not identified in the genomes of these species. FISH analysis using Rex1 detected different distribution patterns, L. elongatus, L. macrocephalus, and L. obtusidens had clusters in the terminal regions, whereas the signals were dispersed throughout all of the chromosomes with some signals in the terminal position in other species. The Rex3 signals were found mainly in the terminal positions in all the chromosomes of all species. The W chromosomes of L. elongatus, L. macrocephalus, and L. obtusidens contained the Rex1 and Rex3 signal in an interstitial position. These results suggest the emergence of different activity levels for these elements during the evolution of the species analyzed. Despite the conserved karyotype macrostructure species Leporinus often discussed, our results show some variation in hybridization patterns, particularly between the species with specific patterns in their sex chromosomes and species without this differentiated system.
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Affiliation(s)
- Rafael Splendore de Borba
- Instituto de Biociências; Universidade Estadual Paulista (UNESP) "Julio de Mesquita Filho," Rio Claro; Departamento de Biologia; Laboratório de Citogenética; Rio Claro, SP Brazil
| | | | - Patrícia Pasquali Parise-Maltempi
- Instituto de Biociências; Universidade Estadual Paulista (UNESP) "Julio de Mesquita Filho," Rio Claro; Departamento de Biologia; Laboratório de Citogenética; Rio Claro, SP Brazil
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34
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Gornung E. Twenty years of physical mapping of major ribosomal RNA genes across the teleosts: A review of research. Cytogenet Genome Res 2013; 141:90-102. [PMID: 24080951 DOI: 10.1159/000354832] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Molecular cytogenetic data on the number and position of 45S ribosomal RNA genes (rDNA; located in nucleolus organizing regions, NORs) detected by FISH in 330 species of 77 families and 22 orders of bony fishes (Teleostei) and, additionally, 11 species of basal ray-finned fishes are compiled and analyzed. The portion of species with single rDNA sites in the sample amounts to 72%. The percentage of species with multiple NORs decreases with increasing numbers of rDNA loci per genome, i.e. scarcely 3% of species carry 4 or more rDNA-bearing chromosome pairs. 43% of all rDNA sites analyzed occur terminally on the short arms of chromosomes or constitute them. In general, terminal rDNA sites account for 87% of all examined cases. Interspecific variation in the location of single rDNA sites among related taxa, polymorphisms of multiple NORs in some groups of teleosts and analytical outcomes on the subject are reviewed.
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Affiliation(s)
- E Gornung
- 'Charles Darwin' Department of Biology and Biotechnologies, University of Rome 'La Sapienza', Rome, Italy
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35
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Chromosomal organization of repetitive DNA sequences in Astyanax bockmanni (Teleostei, Characiformes): dispersive location, association and co-localization in the genome. Genetica 2013; 141:329-36. [DOI: 10.1007/s10709-013-9732-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 08/21/2013] [Indexed: 10/26/2022]
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36
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Voltolin TA, Mendonça BB, Ferreira DC, Senhorini JA, Foresti F, Porto-Foresti F. Chromosomal location of retrotransposable REX 1 in the genomes in five Prochilodus (Teleostei: Characiformes. Mob Genet Elements 2013; 3:e25846. [PMID: 24195015 PMCID: PMC3812791 DOI: 10.4161/mge.25846] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 07/13/2013] [Accepted: 07/22/2013] [Indexed: 01/14/2023] Open
Abstract
Transposable elements are repetitive DNA sequences comprising a group of segments able to move and carry sequences within the genome. Studies involving comparative genomics have revealed that most vertebrates have different populations of transposable elements with significant differences among species of the same lineage. Few studies have been conducted in fish, the most diverse group of vertebrates, with the objective to locate different types of transposable elements. Therefore, this study proposed to map the retrotransposable element Rex1 applying Fluorescent in situ Hybridization (FISH) in five species of the genus Prochilodus (Prochilodus argenteus, Prochilodus brevis, Prochilodus costatus, Prochilodus lineatus and Prochilodus nigricans). After the application of the Rex1 probe, scattered markings were found throughout the genome of analyzed species, and also the presence of small clusters located in the centromeric and telomeric regions coincident with the heterochromatin distribution pattern. This was the first description of the retrotransposable element Rex1 in Prochilodus genome seeking for a better understanding of the distribution pattern of these retrotransposons in the genome of teleost fish.
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Affiliation(s)
- Tatiana Aparecida Voltolin
- Departamento Ciências Biológicas; Faculdade de Ciências; Universidade Estadual Paulista (UNESP); Campus de Bauru; Bauru, São Paulo Brazil
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