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Garcia S, Kovarik A, Maiwald S, Mann L, Schmidt N, Pascual-Díaz JP, Vitales D, Weber B, Heitkam T. The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics. Mol Biol Evol 2024; 41:msae025. [PMID: 38306580 PMCID: PMC10946416 DOI: 10.1093/molbev/msae025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/06/2023] [Accepted: 01/29/2024] [Indexed: 02/04/2024] Open
Abstract
Although both are salient features of genomes, at first glance ribosomal DNAs and transposable elements are genetic elements with not much in common: whereas ribosomal DNAs are mainly viewed as housekeeping genes that uphold all prime genome functions, transposable elements are generally portrayed as selfish and disruptive. These opposing characteristics are also mirrored in other attributes: organization in tandem (ribosomal DNAs) versus organization in a dispersed manner (transposable elements); evolution in a concerted manner (ribosomal DNAs) versus evolution by diversification (transposable elements); and activity that prolongs genomic stability (ribosomal DNAs) versus activity that shortens it (transposable elements). Re-visiting relevant instances in which ribosomal DNA-transposable element interactions have been reported, we note that both repeat types share at least four structural and functional hallmarks: (1) they are repetitive DNAs that shape genomes in evolutionary timescales, (2) they exchange structural motifs and can enter co-evolution processes, (3) they are tightly controlled genomic stress sensors playing key roles in senescence/aging, and (4) they share common epigenetic marks such as DNA methylation and histone modification. Here, we give an overview of the structural, functional, and evolutionary characteristics of both ribosomal DNAs and transposable elements, discuss their roles and interactions, and highlight trends and future directions as we move forward in understanding ribosomal DNA-transposable element associations.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, 08038 Barcelona, Catalonia, Spain
| | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
| | - Sophie Maiwald
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Ludwig Mann
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Nicola Schmidt
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | | | - Daniel Vitales
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica–Unitat Associada CSIC, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Beatrice Weber
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
- Institute of Biology, NAWI Graz, Karl-Franzens-Universität, A-8010 Graz, Austria
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2
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Golub NV, Golub VB, Anokhin BA, Kuznetsova VG. Comparative Cytogenetics of Lace Bugs (Tingidae, Heteroptera): New Data and a Brief Overview. INSECTS 2022; 13:insects13070608. [PMID: 35886784 PMCID: PMC9324616 DOI: 10.3390/insects13070608] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/01/2022] [Accepted: 07/03/2022] [Indexed: 02/06/2023]
Abstract
The lace bug family Tingidae comprises more than 2600 described species in 318 genera that are classified into the subfamilies Tinginae (about 2500 species and 300 genera), Cantacaderinae, and Vianadinae. We provide data on karyotypes of 16 species belonging to 10 genera of the tribes Tingini and Acalyptaini (Tinginae) studied using conventional chromosome staining and FISH. The species of Tingini possess 2n = 12A + XY, whereas those of Acalyptaini have 2n = 12A + X(0). FISH for 18S rDNA revealed hybridization signals on one of the medium-sized bivalents in species of both tribes. FISH with a telomeric probe TTAGG produced no signals in any species. In addition, we provide a list of all data obtained to date on Tingidae karyotypes, which includes 60 species from 22 genera of Tinginae. The subfamily is highly conservative in relation to the number and size of autosomes, whereas it shows diversity in the number and chromosomal distribution of the rDNA arrays, which may be located either on a pair of autosomes (the predominant and supposedly ancestral pattern), on one or both sex chromosomes, or on an autosome pair and the X. The absence of the “insect” telomeric sequence TTAGG in all species implies that Tinginae have some other, yet unknown, telomere organization.
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Affiliation(s)
- Natalia V. Golub
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya emb.1, St. Petersburg 199034, Russia; (B.A.A.); (V.G.K.)
- Department of Zoology and Parasitology, Voronezh State University, Universitetskaya sq.1, Voronezh 394006, Russia;
- Correspondence: ; Tel.: +7-812-323-5197
| | - Viktor B. Golub
- Department of Zoology and Parasitology, Voronezh State University, Universitetskaya sq.1, Voronezh 394006, Russia;
| | - Boris A. Anokhin
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya emb.1, St. Petersburg 199034, Russia; (B.A.A.); (V.G.K.)
| | - Valentina G. Kuznetsova
- Department of Karyosystematics, Zoological Institute, Russian Academy of Sciences, Universitetskaya emb.1, St. Petersburg 199034, Russia; (B.A.A.); (V.G.K.)
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Chen H, Xue J, Zhang Z, Zhang G, Xu X, Li H, Zhang R, Ullah N, Chen L, Amanullah, Zang Z, Lai S, He X, Li W, Guan M, Li J, Chen L, Deng C. High-speed rail model reveals the gene tandem amplification mediated by short repeated sequence in eukaryote. Sci Rep 2022; 12:2289. [PMID: 35145182 PMCID: PMC8831618 DOI: 10.1038/s41598-022-06250-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/24/2022] [Indexed: 02/08/2023] Open
Abstract
The occurrence of gene duplication/amplification (GDA) provide potential material for adaptive evolution with environmental stress. Several molecular models have been proposed to explain GDA, recombination via short stretches of sequence similarity plays a crucial role. By screening genomes for such events, we propose a “SRS (short repeated sequence) *N + unit + SRS*N” amplified unit under USCE (unequal sister-chromatid exchange) for tandem amplification mediated by SRS with different repeat numbers in eukaryotes. The amplified units identified from 2131 well-organized amplification events that generate multi gene/element copy amplified with subsequent adaptive evolution in the respective species. Genomic data we analyzed showed dynamic changes among related species or subspecies or plants from different ecotypes/strains. This study clarifies the characteristics of variable copy number SRS on both sides of amplified unit under USCE mechanism, to explain well-organized gene tandem amplification under environmental stress mediated by SRS in all eukaryotes.
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Affiliation(s)
- Haidi Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Jingwen Xue
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Zhenghou Zhang
- The Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
| | - Geyu Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Xinyuan Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - He Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Ruxue Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Najeeb Ullah
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Lvxing Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Amanullah
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Zhuqing Zang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Shanshan Lai
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China
| | - Ximiao He
- Department of Physiology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.,Center for Genomics and Proteomics Research, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.,Hubei Key Laboratory of Drug Target Research and Pharmacodynamic Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Wei Li
- Department of Dermatovenereology, Institutes for Systems Genetics, Rare Disease Center, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang Street, Chengdu, 610041, Sichuan, China
| | - Miao Guan
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China.
| | - Jingyi Li
- M.D. Department of Dermatology and Venereology, West China Hospital of Sichuan University, No. 37 Guo Xue Lane, Chengdu, 610041, China.
| | - Liangbiao Chen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Ministry of Education), Institute of Experimental Pathology, Shanghai Ocean University, Shanghai, 201306, China.
| | - Cheng Deng
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Rd., Nanjing, 210023, China.
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Menezes RST, Cabral-de-Mello DC, Milani D, Bardella VB, Almeida EAB. The relevance of chromosome fissions for major ribosomal DNA dispersion in hymenopteran insects. J Evol Biol 2021; 34:1466-1476. [PMID: 34331340 DOI: 10.1111/jeb.13909] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/04/2021] [Accepted: 07/28/2021] [Indexed: 01/20/2023]
Abstract
Ribosomal DNA (rDNA) loci are essential for cellular metabolism due to their participation in ribosome biogenesis. Although these genes have been widely cytogenetically mapped, the evolutionary mechanisms behind their variability in number and chromosomal location remain elusive, even in well-known biological groups, such as ants, bees and wasps (Insecta: Hymenoptera). To address this question in Hymenoptera and therefore advance the understanding of rDNA evolution in insects in general, we integrated molecular cytogenetic data, a phylogenomic framework, model-based predictions and genome sequencing. Hence, we assessed the main evolutionary trends shaping the chromosomal distribution of rDNA loci in Hymenoptera. We noticed the conservation of one site of rDNA per haploid genome, suggesting that a single 45S rDNA locus is the putative ancestral pattern for aculeate Hymenoptera. Moreover, our results highlighted a nonrandom distribution of rDNA in Hymenoptera karyotypes, as well as a lineage-specific preferential location. The proximal location of rDNA is favoured in species with multiple loci and in the two families of Hymenoptera that show the highest range of chromosome numbers: Formicidae and Vespidae. We propose that chromosome fissions have played a crucial role in the distribution pattern of rDNA loci through the evolutionary diversification of Hymenoptera. Moreover, our genomic analysis of two species, one with a single locus of rDNA and one with multiple loci, supported that loci multiplication is followed by sequence divergence. Our results provide detailed information about the number and chromosomal position of rDNA in Hymenoptera and, therefore, broaden our knowledge regarding rDNA evolutionary dynamics in insects.
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Affiliation(s)
- Rodolpho S T Menezes
- Laboratório de Biologia Comparada e Abelhas, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras (FFCLRP), Universidade de São Paulo (USP), Ribeirão Preto, Brazil
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Vanessa B Bardella
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Eduardo A B Almeida
- Laboratório de Biologia Comparada e Abelhas, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras (FFCLRP), Universidade de São Paulo (USP), Ribeirão Preto, Brazil
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Ribeiro T, Nascimento J, Santos A, Félix LP, Guerra M. Origin and evolution of highly polymorphic rDNA sites in Alstroemeria longistaminea (Alstroemeriaceae) and related species. Genome 2021; 64:833-845. [PMID: 33852822 DOI: 10.1139/gen-2020-0159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Alstroemeria (Alstroemeriaceae) displays a conserved and highly asymmetric karyotype, where most rDNA sites can be properly recognized by the size and morphology of the chromosomes. We analyzed the intraspecific variation of rDNA sites in A. longistaminea and compared with their distribution in other species (A. caryophyllaea and A. piauhyensis) and a representative of a sister genus, Bomarea edulis. All three species of Alstroemeria presented 2n = 16, and one to six B chromosomes were found in some individuals of A. longistaminea. There was a set of 12 conserved rDNA sites (four 5S and eight 35S) and up to 11 variable sites. B chromosomes were almost entirely covered by 35S signals, coupled with tiny 5S sites. Noteworthy, most rDNA sites found in A. caryophyllaea and A. piauhyensis were localized in chromosome positions similar to those in A. longistaminea, suggesting the existence of conserved hotspots for rDNA accumulation. Some of these hotspots were absent in Chilean Alstromeria as well in B. edulis. We propose that insertions of rDNA sequences on chromosomes do not occur randomly but rather on preferential sites or hotspots for insertions. The maintenance of these arrays, however, may be favored/constrained by different factors, resulting in stable or polymorphic sites.
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Affiliation(s)
- Tiago Ribeiro
- Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Departamento de Botânica, Recife, Pernambuco, Brasil
| | - Jéssica Nascimento
- Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Departamento de Botânica, Recife, Pernambuco, Brasil
| | - Amanda Santos
- Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Departamento de Botânica, Recife, Pernambuco, Brasil
| | - Leonardo P Félix
- Universidade Federal da Paraíba, Departamento de Biociências, Campus II, Areia, Paraíba, Brasil
| | - Marcelo Guerra
- Laboratório de Citogenética e Evolução Vegetal, Universidade Federal de Pernambuco, Departamento de Botânica, Recife, Pernambuco, Brasil
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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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Piscor D, Paiz LM, Baumgärtner L, Cerqueira FJ, Fernandes CA, Lui RL, Parise-Maltempi PP, Margarido VP. Chromosomal mapping of repetitive sequences in Hyphessobrycon eques (Characiformes, Characidae): a special case of the spreading of 5S rDNA clusters in a genome. Genetica 2020; 148:25-32. [PMID: 31997050 DOI: 10.1007/s10709-020-00086-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 10/28/2019] [Accepted: 01/20/2020] [Indexed: 01/23/2023]
Abstract
Cytogenetic data showed a variation in diploid chromosome number in the genus Hyphessobrycon ranging from 2n = 46 to 52, and studies involving repetitive DNA sequences are scarce in representatives of this genus. The purpose of this paper was the chromosomal mapping of repetitive sequences (rDNA, histone genes, U snDNA and microsatellites) and investigation of the amplification of 5S rDNA clusters in the Hyphessobrycon eques genome. Two H. eques populations displayed 2n = 52 chromosomes, with the acrocentric pair No. 24 bearing Ag-NORs corresponding with CMA3+/DAPI-. FISH with a 18S rDNA probe identified the NORs on the short (p) arms of the acrocentric pairs Nos. 22 and 24. The 5S rDNA probe visualized signals on almost all chromosomes in genomes of individuals from both populations (40 signals); FISH with H3 histone probe identified two chromosome pairs, with the pericentromeric location of signals; FISH with a U2 snDNA probe identified one chromosome pair bearing signals, on the interstitial chromosomal region. The mononucleotide (A), dinucleotide (CA) and tetranucleotide (GATA) repeats were observed on the centromeric/pericentromeric and/or terminal positions of all chromosomes, while the trinucleotide (CAG) repeat showed signals on few chromosomes. Molecular analysis of 5S rDNA and non-transcribed spacers (NTS) showed microsatellites (GATA and A repeats) and a fragment of retrotransposon (SINE3/5S-Sauria) inside the sequences. This study expanded the available cytogenetic data for H. eques and demonstrated to the dispersion of the 5S rDNA sequences on almost all chromosomes.
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Affiliation(s)
- Diovani Piscor
- Centro de Ciências Biológicas e da Saúde, Laboratório de Citogenética, Universidade Estadual do Oeste do Paraná (UNIOESTE), Rua Universitária, 2069, Cascavel, PR, ZIP: 85819-110, Brazil. .,Universidade Estadual de Mato Grosso do Sul (UEMS), Unidade de Mundo Novo, BR 163, Km 20.2, Mundo Novo, MS, ZIP: 79980-000, Brazil.
| | - Leonardo Marcel Paiz
- Centro de Ciências Biológicas e da Saúde, Laboratório de Citogenética, Universidade Estadual do Oeste do Paraná (UNIOESTE), Rua Universitária, 2069, Cascavel, PR, ZIP: 85819-110, Brazil
| | - Lucas Baumgärtner
- Centro de Ciências Biológicas e da Saúde, Laboratório de Citogenética, Universidade Estadual do Oeste do Paraná (UNIOESTE), Rua Universitária, 2069, Cascavel, PR, ZIP: 85819-110, Brazil
| | - Fiorindo José Cerqueira
- Centro de Ciências Biológicas e da Saúde, Laboratório de Citogenética, Universidade Estadual do Oeste do Paraná (UNIOESTE), Rua Universitária, 2069, Cascavel, PR, ZIP: 85819-110, Brazil
| | - Carlos Alexandre Fernandes
- Universidade Estadual de Mato Grosso do Sul (UEMS), Unidade de Mundo Novo, BR 163, Km 20.2, Mundo Novo, MS, ZIP: 79980-000, Brazil
| | - Roberto Laridondo Lui
- Centro de Ciências Biológicas e da Saúde, Laboratório de Citogenética, Universidade Estadual do Oeste do Paraná (UNIOESTE), Rua Universitária, 2069, Cascavel, PR, ZIP: 85819-110, Brazil
| | - Patricia Pasquali Parise-Maltempi
- Instituto de Biociências, Departamento de Biologia, Laboratório de Citogenética, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Av. 24A, 1515, Rio Claro, SP, ZIP: 13506-900, Brazil
| | - Vladimir Pavan Margarido
- Centro de Ciências Biológicas e da Saúde, Laboratório de Citogenética, Universidade Estadual do Oeste do Paraná (UNIOESTE), Rua Universitária, 2069, Cascavel, PR, ZIP: 85819-110, Brazil
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Grabowska AI, Boroń A, Kirtiklis L, Spóz A, Juchno D, Kotusz J. Chromosomal inheritance of parental rDNAs distribution pattern detected by FISH in diploid F 1 hybrid progeny of Cobitis (Teleostei, Cobitidae) species has non-Mendelian character. JOURNAL OF FISH BIOLOGY 2020; 96:261-273. [PMID: 31755097 DOI: 10.1111/jfb.14216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 11/21/2019] [Indexed: 06/10/2023]
Abstract
This study was conducted to describe the major and the minor rDNA chromosome distribution in the spined loach Cobitis taenia (2n = 48) and the Danubian loach Cobitis elongatoides (2n = 50), and their laboratory-produced diploid reciprocal F1 hybrid progeny. It was tested by fluorescence in situ hybridisation (FISH) whether the number of 28s and 5s rDNA sites in the karyotypes of diploid hybrids corresponds to the expectations resulting from Mendelian ratio and if nucleolar organiser regions (NOR)were inherited from both parents or nucleolar dominance can be observed in the induced F1 hybrid progeny. Ten (females) or twelve (males) 28s rDNA loci were located in nine uniarm chromosomes of C. taenia. Two of such loci terminally bounded on one acrocentric chromosome were unique and indicated as specific for this species. Large 5s rDNA clusters were located on two acrocentric chromosomes. In C. elongatoides of both sexes, six NOR sites in terminal regions on six meta-submetacentric chromosomes and two 5s rDNA sites on large submetacentrics were detected. The F1 hybrid progeny (2n = 49) was characterised by the intermediate karyotype with the sites of ribosome synthesis on chromosomes inherited from both parents without showing nucleolar dominance. 5s rDNA sites were detected on large submetacentric and two acrocentric chromosomes. The observed number of both 28s and 5s rDNAs signals in F1 diploid Cobitis hybrids was disproportionally inherited from the two parental species, showing inconsistency with the Mendelian ratios. The presented rDNA patterns indicate some marker chromosomes that allow the species of the parental male and female to be recognised in hybrid progeny. The 5s rDNA was found to be a particularly effective diagnostic marker of C. elongatoides to partially discern genomic composition of diploid Cobitis hybrids and presumably allopolyploids resulting from their backcrossing with one of the parental species. Thus, the current study provides insight into the extent of rDNA heredity in Cobitis chromosomes and their cytotaxonomic character.
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Affiliation(s)
- Anna I Grabowska
- Department of Zoology, University of Warmia and Mazury, Olsztyn, Poland
| | - Alicja Boroń
- Department of Zoology, University of Warmia and Mazury, Olsztyn, Poland
| | - Lech Kirtiklis
- Department of Zoology, University of Warmia and Mazury, Olsztyn, Poland
| | - Aneta Spóz
- Department of Zoology, University of Warmia and Mazury, Olsztyn, Poland
| | - Dorota Juchno
- Department of Zoology, University of Warmia and Mazury, Olsztyn, Poland
| | - Jan Kotusz
- Museum of Natural History, University of Wroclaw, Wroclaw, Poland
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Zhan S, Fang G, Cai M, Kou Z, Xu J, Cao Y, Bai L, Zhang Y, Jiang Y, Luo X, Xu J, Xu X, Zheng L, Yu Z, Yang H, Zhang Z, Wang S, Tomberlin JK, Zhang J, Huang Y. Genomic landscape and genetic manipulation of the black soldier fly Hermetia illucens, a natural waste recycler. Cell Res 2020; 30:50-60. [PMID: 31767972 PMCID: PMC6951338 DOI: 10.1038/s41422-019-0252-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/22/2019] [Indexed: 11/09/2022] Open
Abstract
The black soldier fly (BSF), Hermetia illucens (Diptera: Stratiomyidae), is renowned for its bioconversion of organic waste into a sustainable source of animal feed. We report a high-quality genome of 1.1 Gb and a consensus set of 16,770 gene models for this beneficial species. Compared to those of other dipteran species, the BSF genome has undergone a substantial expansion in functional modules related to septic adaptation, including immune system factors, olfactory receptors, and cytochrome P450s. We further profiled midgut transcriptomes and associated microbiomes of BSF larvae fed with representative types of organic waste. We find that the pathways related to digestive system and fighting infection are commonly enriched and that Firmicutes bacteria dominate the microbial community in BSF across all diets. To extend its potential practical applications, we further developed an efficient CRISPR/Cas9-based gene editing approach and implemented this to yield flightless and enhanced feeding capacity phenotypes, both of which could expand BSF production capabilities. Our study provides valuable genomic and technical resources for optimizing BSF lines for industrialization.
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Affiliation(s)
- Shuai Zhan
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Gangqi Fang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Minmin Cai
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zongqing Kou
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jun Xu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yanghui Cao
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Liang Bai
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yixiang Zhang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yongmao Jiang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xingyu Luo
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Xu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xia Xu
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Longyu Zheng
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Ziniu Yu
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hong Yang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Institute of Entomology, School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Zhijian Zhang
- School of Economics, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, China
| | - Sibao Wang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jeffery K Tomberlin
- Department of Entomology, Texas A&M University, 2475 TAMU, College Station, TX, 77845, USA.
| | - Jibin Zhang
- State Key Laboratory of Agricultural Microbiology, National Engineering Research Center of Microbial Pesticides, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
| | - Yongping Huang
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
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10
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Li S, Xie L, Xiao J, Yuan L, Zhou T, Luo K, Zhang C, Zhao R, Tao M, Liu S. Diploid hybrid fish derived from the cross between female Bleeker's yellow tail and male topmouth culter, two cyprinid fishes belonging to different subfamilies. BMC Genet 2019; 20:80. [PMID: 31646976 PMCID: PMC6813094 DOI: 10.1186/s12863-019-0781-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/26/2019] [Indexed: 01/09/2023] Open
Abstract
Background Bleeker’s yellow tail (Xenocypris davidi Bleeker, YT) and topmouth culter (Culter alburnus Basilewsky, TC) are both famous and important economic freshwater fish in China. YT, a kind of omnivorous fish, has strong resistance. TC, a kind of carnivorous fish, has high-quality meat but poor resistance. Distant hybridization can integrate the advantages of both parents. There has been no previous report regarding hybrid fish derived from female YT × male TC. It is expected that hybridization of these two kinds of fish will result in F1 hybrids with improved characteristics, such as faster growth rate, stronger resistance, and high-quality meat, which are of great significance in fish genetic breeding. Results In this study, we investigated the main biological characteristics of diploid hybrid fish derived from female YT × male TC. The hybrids had an intermediate number of upper lateral line scales between those for YT and TC. The hybrids were diploids with 48 chromosomes and had the same karyotype formula as their parents. The hybrids generated variations in 5S rDNA (designated class IV: 212 bp) and lost specific 5S rDNA derived from the maternal parent (designated class II: 221 bp), which might be related to hybridization. In terms of reproductive traits, all the tested female hybrids exhibited normal gonadal development, and the two-year-old F1 females produced mature eggs. However, all the tested testes of the male hybrids could not produce mature sperm. It is possible that the hybrid lineage will be established by back-crossing the fertile female hybrids and their parents. Conclusions Obtaining a fertile female hybrid fish made the creation of a new type of fish possible, which was significant in fish genetic breeding.
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Affiliation(s)
- Shengnan Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Lihua Xie
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Jun Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Liujiao Yuan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Tian Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Kaikun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, China. .,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China.
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, Hunan, China. .,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, China.
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11
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Majtánová Z, Indermaur A, Nyom ARB, Ráb P, Musilova Z. Adaptive Radiation from a Chromosomal Perspective: Evidence of Chromosome Set Stability in Cichlid Fishes (Cichlidae: Teleostei) from the Barombi Mbo Lake, Cameroon. Int J Mol Sci 2019; 20:ijms20204994. [PMID: 31601021 PMCID: PMC6834198 DOI: 10.3390/ijms20204994] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/04/2019] [Accepted: 10/07/2019] [Indexed: 12/11/2022] Open
Abstract
Cichlid fishes are the subject of scientific interest because of their rapid adaptive radiation, resulting in extensive ecological and taxonomic diversity. In this study, we examined 11 morphologically distinct cichlid species endemic to Barombi Mbo, the largest crater lake in western Cameroon, namely Konia eisentrauti, Konia dikume, Myaka myaka, Pungu maclareni, Sarotherodon steinbachi, Sarotherodon lohbergeri, Sarotherodon linnellii, Sarotherodon caroli, Stomatepia mariae, Stomatepia pindu, and Stomatepia mongo. These species supposedly evolved via sympatric ecological speciation from a common ancestor, which colonized the lake no earlier than one million years ago. Here we present the first comparative cytogenetic analysis of cichlid species from Barombi Mbo Lake using both conventional (Giemsa staining, C-banding, and CMA3/DAPI staining) and molecular (fluorescence in situ hybridization with telomeric, 5S, and 28S rDNA probes) methods. We observed stability on both macro and micro-chromosomal levels. The diploid chromosome number was 2n = 44, and the karyotype was invariably composed of three pairs of meta/submetacentric and 19 pairs of subtelo/acrocentric chromosomes in all analysed species, with the same numbers of rDNA clusters and distribution of heterochromatin. The results suggest the evolutionary stability of chromosomal set; therefore, the large-scale chromosomal rearrangements seem to be unlikely associated with the sympatric speciation in Barombi Mbo.
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Affiliation(s)
- Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic.
| | - Adrian Indermaur
- Zoological Institute, University of Basel, 4051 Basel, Switzerland.
| | - Arnold Roger Bitja Nyom
- Department of Biological Sciences, University of Ngaoundéré, Ngaoundéré P.O Box 454, Cameroon.
- Department of Management of Fisheries and Aquatic Ecosystems, University of Douala, Douala P.O Box 2701, Cameroon.
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, 27721 Liběchov, Czech Republic.
| | - Zuzana Musilova
- Department of Zoology, Faculty of Science, Charles University in Prague, 12844 Prague, Czech Republic.
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12
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Frade LFDS, Almeida BRRD, Milhomem-Paixão SSR, Ready JS, Nagamachi CY, Pieczarka JC, Noronha RCR. Karyoevolution of Crenicichla heckel 1840 (Cichlidae, Perciformes): a process mediated by inversions. Biol Open 2019; 8:bio.041699. [PMID: 31036749 PMCID: PMC6550074 DOI: 10.1242/bio.041699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Crenicichla (Cichliformes, Cichlidae) present a highly conserved diploid number 2n=48 with fundamental numbers varying between 52 and 62. We analyzed four species in order to investigate the role of repetitive DNA in chromosome evolution in the genus. Crenicichla johanna, Crenicichla cf. saxatilis and Crenicichla cf. regani have 2n=48 (8 m/sm and 40st/a) and FN=56, while Crenicichla sp. ‘Xingu I’ has 2n=48 (48 st/a) and FN=48. Different patterns of constitutive heterochromatin distribution were observed including pericentric, interstitial and whole arm C bands. A single chromosome bears 18S rDNA clusters in most species, except C. johanna, where population variation exists in terms of the quantity and distribution of clusters and their association with interstitial telomeric sequences. All species showed hybridization of 5S rDNA sequences in an interstitial region on an acrocentric chromosome pair. The karyotypic differences and maintenance of the diploid number supports chromosome evolution mediated by inversions in Crenicichla. The telomeric and 18S rDNA sequence association in various chromosomes of C. johanna are proposed to represent hotspots for breakage, favoring intra-chromosomal rearrangements. The results suggest that repetitive sequences can contribute to microstructural cytogenetic diversity in Crenicichla. Summary: This paper has a great importance for understanding karyotype evolutionary dynamics in neotropical freshwater fish, focusing on repetitive DNA and the role of inversions in Crenicichla.
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Affiliation(s)
- Luan Felipe da Silva Frade
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
| | - Bruno Rafael Ribeiro de Almeida
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
| | - Susana Suely Rodrigues Milhomem-Paixão
- Instituto Federal de Educação, Ciência e Tecnologia de Goiás, campus Valparaıso de Goiás, BR-040, km 6, Avenida Saia Velha, S/N, Área 8, Parque Esplanada V. 72.876-601, Valparaíso de Goiás, Goiás, Brasil
| | - Jonathan Stuart Ready
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
| | - Cleusa Yoshiko Nagamachi
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
| | - Julio Cesar Pieczarka
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
| | - Renata Coelho Rodrigues Noronha
- Centro de Estudos Avançados da Biodiversidade, Universidade Federal do Pará, Campus Guamá, Rua Augusto Corrêa, n° 01. Guamá, Belém, Pará, Brasil
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13
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Symonová R. Integrative rDNAomics-Importance of the Oldest Repetitive Fraction of the Eukaryote Genome. Genes (Basel) 2019; 10:genes10050345. [PMID: 31067804 PMCID: PMC6562748 DOI: 10.3390/genes10050345] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 04/17/2019] [Accepted: 04/25/2019] [Indexed: 02/06/2023] Open
Abstract
Nuclear ribosomal RNA (rRNA) genes represent the oldest repetitive fraction universal to all eukaryotic genomes. Their deeply anchored universality and omnipresence during eukaryotic evolution reflects in multiple roles and functions reaching far beyond ribosomal synthesis. Merely the copy number of non-transcribed rRNA genes is involved in mechanisms governing e.g., maintenance of genome integrity and control of cellular aging. Their copy number can vary in response to environmental cues, in cellular stress sensing, in development of cancer and other diseases. While reaching hundreds of copies in humans, there are records of up to 20,000 copies in fish and frogs and even 400,000 copies in ciliates forming thus a literal subgenome or an rDNAome within the genome. From the compositional and evolutionary dynamics viewpoint, the precursor 45S rDNA represents universally GC-enriched, highly recombining and homogenized regions. Hence, it is not accidental that both rDNA sequence and the corresponding rRNA secondary structure belong to established phylogenetic markers broadly used to infer phylogeny on multiple taxonomical levels including species delimitation. However, these multiple roles of rDNAs have been treated and discussed as being separate and independent from each other. Here, I aim to address nuclear rDNAs in an integrative approach to better assess the complexity of rDNA importance in the evolutionary context.
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Affiliation(s)
- Radka Symonová
- Faculty of Science, Department of Biology, University of Hradec Králové, 500 03 Hradec Králové, Czech Republic.
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14
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Menezes RST, Gazoni T, Costa MA. Cytogenetics of warrior wasps (Vespidae:Synoeca) reveals intense evolutionary dynamics of ribosomal DNA clusters and an unprecedented number of microchromosomes in Hymenoptera. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Rodolpho S T Menezes
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras – Universidade de São Paulo (FFCLRP/USP), Ribeirão Preto, SP, Brazil
| | - Thiago Gazoni
- Departamento de Biologia – Universidade Estadual Paulista (UNESP), Instituto de Biociências, Rio Claro, SP, Brazil
| | - Marco A Costa
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
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15
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Remarkable sequence polymorphisms in 18S rDNA of Pleuronichthys cornutus (Pleuronectiformes: Pleuronectidae). Gene 2018; 677:251-258. [DOI: 10.1016/j.gene.2018.07.055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 07/15/2018] [Accepted: 07/19/2018] [Indexed: 11/22/2022]
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16
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Piscor D, Pozzobon APB, Fernandes CA, Centofante L, Parise-Maltempi PP. Molecular Clock as Insight to Estimate the Evolutionary History and Times of Divergence for 10 Nominal Astyanax Species (Characiformes, Characidae): An Evolutionary Approach in Species with 2n = 36, 46, 48, and 50 Chromosomes. Zebrafish 2018; 16:98-105. [PMID: 30358520 DOI: 10.1089/zeb.2018.1647] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Astyanax is a genus with a wide distribution ranging from the south United States to north of Patagonia (Argentina). The available cytogenetic data on Astyanax indicate a high karyotypic diversity, with diploid number of 36-52 chromosomes, presence of B chromosomes, heterochromatin polymorphism, and variations with respect to the number and localization of nucleolar organizer regions (NORs) and 18S and 5S ribosomal DNA sites. In the present study, we estimated the evolutionary history and times of divergence for 10 nominal Astyanax species from the South and Central/North American (Cna) continents, which present distinct chromosomal characteristics, based on molecular clocks inferred from mitochondrial DNA sequence. The molecular clock results indicate the origin of three distinct clades (Humeral dark spot [Hds]; Diffuse humeral spot [Dhs]; Cna group) during the late Miocene about 11.2 million years ago (Mya). Thus, Astyanax mexicanus (Cna) represent a species that diverged a long time ago (∼8.6 Mya) from the Hds group, and Astyanax schubarti is the oldest species (∼6.5 Mya) among the Dhs species.
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Affiliation(s)
- Diovani Piscor
- 1 Laboratório de Citogenética, Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Rio Claro, Brazil.,2 Universidade Estadual de Mato Grosso do Sul (UEMS), Unidade de Mundo Novo, Mundo Novo, Brazil
| | - Allan Pierre Bonetti Pozzobon
- 3 Universidade Federal do Rio de Janeiro (UFRJ), Núcleo em Ecologia e Desenvolvimento Socioambiental de Macaé (NUPEM/UFRJ), Macaé, Brazil
| | | | - Liano Centofante
- 4 Laboratório de Genética Animal, Departamento de Biologia e Zoologia, Instituto de Biociências, Universidade Federal de Mato Grosso (UFMT), Cuiabá, Brazil
| | - Patricia Pasquali Parise-Maltempi
- 1 Laboratório de Citogenética, Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP), Rio Claro, Brazil
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17
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Sember A, Bohlen J, Šlechtová V, Altmanová M, Pelikánová Š, Ráb P. Dynamics of tandemly repeated DNA sequences during evolution of diploid and tetraploid botiid loaches (Teleostei: Cobitoidea: Botiidae). PLoS One 2018; 13:e0195054. [PMID: 29590207 PMCID: PMC5874072 DOI: 10.1371/journal.pone.0195054] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 03/15/2018] [Indexed: 12/16/2022] Open
Abstract
Polyploidization has played an important role in the evolution of vertebrates, particularly at the base of Teleostei-an enormously successful ray-finned fish group with additional genome doublings on lower taxonomic levels. The investigation of post-polyploid genome dynamics might provide important clues about the evolution and ecology of respective species and can help to decipher the role of polyploidy per se on speciation. Few studies have attempted to investigate the dynamics of repetitive DNA sequences in the post-polyploid genome using molecular cytogenetic tools in fishes, though recent efforts demonstrated their usefulness. The demonstrably monophyletic freshwater loach family Botiidae, branching to evolutionary diploid and tetraploid lineages separated >25 Mya, offers a suited model group for comparing the long-term repetitive DNA evolution. For this, we integrated phylogenetic analyses with cytogenetical survey involving Giemsa- and Chromomycin A3 (CMA3)/DAPI stainings and fluorescence in situ hybridization with 5S/45S rDNA, U2 snDNA and telomeric probes in representative sample of 12 botiid species. The karyotypes of all diploids were composed of 2n = 50 chromosomes, while majority of tetraploids had 2n = 4x = 100, with only subtle interspecific karyotype differences. The exceptional karyotype of Botia dario (2n = 4x = 96) suggested centric fusions behind the 2n reduction. Variable patterns of FISH signals revealed cases of intraspecific polymorphisms, rDNA amplification, variable degree of correspondence with CMA3+ sites and almost no phylogenetic signal. In tetraploids, either additivity or loci gain/loss was recorded. Despite absence of classical interstitial telomeric sites, large blocks of interspersed rDNA/telomeric regions were found in diploids only. We uncovered different molecular drives of studied repetitive DNA classes within botiid genomes as well as the advanced stage of the re-diploidization process in tetraploids. Our results may contribute to link genomic approach with molecular cytogenetic analyses in addressing the origin and mechanism of this polyploidization event.
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Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Jörg Bohlen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Vendula Šlechtová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Marie Altmanová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, Czech Republic
| | - Šárka Pelikánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, Czech Republic
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18
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Uncovering the molecular organization of unusual highly scattered 5S rDNA: The case of Chariesterus armatus (Heteroptera). Gene 2018; 646:153-158. [DOI: 10.1016/j.gene.2017.12.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 12/11/2017] [Accepted: 12/15/2017] [Indexed: 10/18/2022]
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19
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Symonová R, Howell WM. Vertebrate Genome Evolution in the Light of Fish Cytogenomics and rDNAomics. Genes (Basel) 2018; 9:genes9020096. [PMID: 29443947 PMCID: PMC5852592 DOI: 10.3390/genes9020096] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 12/19/2022] Open
Abstract
To understand the cytogenomic evolution of vertebrates, we must first unravel the complex genomes of fishes, which were the first vertebrates to evolve and were ancestors to all other vertebrates. We must not forget the immense time span during which the fish genomes had to evolve. Fish cytogenomics is endowed with unique features which offer irreplaceable insights into the evolution of the vertebrate genome. Due to the general DNA base compositional homogeneity of fish genomes, fish cytogenomics is largely based on mapping DNA repeats that still represent serious obstacles in genome sequencing and assembling, even in model species. Localization of repeats on chromosomes of hundreds of fish species and populations originating from diversified environments have revealed the biological importance of this genomic fraction. Ribosomal genes (rDNA) belong to the most informative repeats and in fish, they are subject to a more relaxed regulation than in higher vertebrates. This can result in formation of a literal 'rDNAome' consisting of more than 20,000 copies with their high proportion employed in extra-coding functions. Because rDNA has high rates of transcription and recombination, it contributes to genome diversification and can form reproductive barrier. Our overall knowledge of fish cytogenomics grows rapidly by a continuously increasing number of fish genomes sequenced and by use of novel sequencing methods improving genome assembly. The recently revealed exceptional compositional heterogeneity in an ancient fish lineage (gars) sheds new light on the compositional genome evolution in vertebrates generally. We highlight the power of synergy of cytogenetics and genomics in fish cytogenomics, its potential to understand the complexity of genome evolution in vertebrates, which is also linked to clinical applications and the chromosomal backgrounds of speciation. We also summarize the current knowledge on fish cytogenomics and outline its main future avenues.
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Affiliation(s)
- Radka Symonová
- Faculty of Science, Department of Biology, University of Hradec Králové, 500 03 Hradec Králové, Czech Republic.
| | - W Mike Howell
- Department of Biological and Environmental Sciences, Samford University, Birmingham, AL 35229, USA.
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Conde-Saldaña CC, Barreto CAV, Villa-Navarro FA, Dergam JA. An Unusual Accumulation of Ribosomal Multigene Families and Microsatellite DNAs in the XX/XY Sex Chromosome System in the Trans-Andean Catfish Pimelodella cf. chagresi (Siluriformes:Heptapteridae). Zebrafish 2017; 15:55-62. [PMID: 29090985 DOI: 10.1089/zeb.2017.1469] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This work constitutes the first cytogenetic characterization of a trans-Andean species of Heptapteridae. The catfish Pimelodella cf. chagresi from the Upper Rio Magdalena was studied, applying standard cytogenetic techniques (Giemsa, C-banding, and argyrophilic nucleolar organizer region [Ag-NOR]) and fluorescence in situ hybridization techniques using repetitive DNA probes: microsatellites (CA15 and GA15) and ribosomal RNA (rRNA) multigene families (18S and 5S recombinant DNA [rDNA] probes). The species showed a unique diploid chromosome number 2n = 50 (32m [metacentrics] +14sm [submetacentrics] +4st [subtelocentrics]) and a XX/XY sex chromosomal system, where the heteromorphic Y-chromosome revealed a conspicuous accumulation of all the assayed domains of repetitive DNA. P. cf. chagresi karyotype shares common features with other Heptapteridae, such as the predominance of metacentric and submetacentric chromosomes, and one pair of subtelomeric nucleolar organizer regions (NORs). These results reflect an independent karyological identity of a trans-Andean species and the relevance of repetitive DNA sequences in the process of sex chromosome differentiation in fish; it is the first case of syntenic accumulation of rRNA multigene families (18S and 5S rDNA) and microsatellite sequences (CA15 and GA15) in a differentiated sex chromosome in Neotropical fish.
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Affiliation(s)
- Cristhian Camilo Conde-Saldaña
- 1 Departamento de Biologia Animal, Universidade Federal de Viçosa , Viçosa, Brazil .,2 Grupo de Investigación en Zoología, Facultad de Ciencias, Universidad del Tolima , Ibagué, Colombia
| | | | | | - Jorge Abdala Dergam
- 1 Departamento de Biologia Animal, Universidade Federal de Viçosa , Viçosa, Brazil
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21
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Han CC, Yen TB, Chen NC, Tseng MC. Cytogenetics of Two Onychostoma Species in Taiwan by Ag-NOR and 18S rDNA Profiles. Zool Stud 2017; 56:e25. [PMID: 31966224 PMCID: PMC6517726 DOI: 10.6620/zs.2017.56-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/05/2017] [Indexed: 11/18/2022]
Abstract
Chiao-Chuan Han, Tsair-Bor Yen, Nian-Cih Chen, and Mei-Chen Tseng (2017) Both Onychostoma barbatulum and O. alticorpus are primary freshwater fish in Taiwan. The former has been developed as an aquaculture species with high economic value, while the latter is a native endemic species in Taiwan. Understanding the cytogenetic information of these two species is necessary for their selected breeding, recovery, and management. In this study, Giemsa staining, silver-binding nucleolar organizer region (Ag-NOR), C-banding, and fluorescence in situ hybridization (FISH) with 18S ribosomal (r)DNA probes were used to analyze the cytogenetic characteristics. Results of Giemsa staining showed that the two Onychostoma species shared the same number of chromosomes, 2n = 50. Respective karyotype formulas of the female and male were 10 m + 22 sm + 10 st + 8 t and 11 m + 22 sm + 10 st + 7 t in O. barbatulum, and 14 m + 18 sm + 8 st + 10 t and 15 m + 18 sm + 8 st + 9 t in O. alticorpus. Karyotypes of both species showed a pair of heteromorphic chromosomes in male fish. Their sex determination should be the XX/XY system. Two pairs of Ag-NORs were found in O. barbatulum, but only one pair occurred in O. alticorpus. C-banding areas were observed on centromeres or telomeres of some chromosomes. FISH revealed different cytogenetic characters between these two species. The above cytogenetic information will contribute to species identification, population recovery, and advantages for breeding and management in the future.
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Affiliation(s)
- Chiao-Chuan Han
- National Museum of Marine Biology and Aquarium, Pingtung 944, Taiwan. E-mail:
- Graduate Institute of Marine Biology, National Dong Hwa University, Hualien 974, Taiwan
| | - Tsair-Bor Yen
- Department of Tropical Agriculture and International Cooperation, National Pingtung
University of Science and Technology, Pingtung 912, Taiwan. E-mail:
| | - Nian-Cih Chen
- Department of Aquaculture, National Pingtung University of Science and Technology,
Pingtung 912, Taiwan
| | - Mei-Chen Tseng
- Department of Aquaculture, National Pingtung University of Science and Technology,
Pingtung 912, Taiwan
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22
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Supiwong W, Jiwyam W, Sreeputhorn K, Maneechot N, Bertollo LAC, Cioffi MB, Getlekha N, Tanomtong A. First report on classical and molecular cytogenetics of archerfish, Toxotes chatareus (Perciformes: Toxotidae). THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0216-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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23
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Bitencourt JA, Sampaio I, Ramos RT, Vicari MR, Affonso PRADM. First Report of Sex Chromosomes in Achiridae (Teleostei: Pleuronectiformes) with Inferences About the Origin of the Multiple X1X1X2X2/X1X2Y System and Dispersal of Ribosomal Genes inAchirus achirus. Zebrafish 2017; 14:90-95. [DOI: 10.1089/zeb.2016.1333] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Iracilda Sampaio
- Institute of Coastal Studies, Federal University of Pará, Bragança, Brazil
| | - Robson T.C. Ramos
- Department of Systematics and Ecology, Federal University of Paraíba, João Pessoa, Brazil
| | - Marcelo Ricardo Vicari
- Department of Genetics, Structural and Molecular Biology, State University of Ponta Grossa, Ponta Grossa, Brazil
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24
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Yano CF, Bertollo LAC, Rebordinos L, Merlo MA, Liehr T, Portela-Bens S, Cioffi MDB. Evolutionary Dynamics of rDNAs and U2 Small Nuclear DNAs in Triportheus (Characiformes, Triportheidae): High Variability and Particular Syntenic Organization. Zebrafish 2017; 14:146-154. [PMID: 28051362 DOI: 10.1089/zeb.2016.1351] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Multigene families correspond to a group of genes tandemly repeated, showing enormous diversity in both number of units and genomic organization. In fishes, unlike rDNAs that have been well explored in cytogenetic studies, U2 small nuclear RNA (snRNA) genes are poorly investigated concerning their chromosomal localization. All Triportheus species (Characiformes, Triportheidae) studied so far carry a ZZ/ZW sex chromosomes system, where the W chromosome contains a huge 18S rDNA cistron. In some species the syntenic organization of rDNAs on autosomes was also verified. To explore this particular organization, we performed three-color-fluorescence in situ hybridization using 5S, 18S rDNA, and U2 snRNA genes as probes in eight Triportheus species. This work represents the first one analyzing the chromosomal distribution of U2 snRNA genes in genomes of Triportheidae. The variability in number of rDNA clusters, and the divergent syntenies for these three multigene families, put in evidence their evolutionary dynamism, revealing a much more complex organization of these genes than previously supposed for closely related species. Our study also provides additional data on the accumulation of repetitive sequences in the sex-specific chromosome. Besides, the chromosomal organization of U2 snDNAs among fish species is also reviewed.
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Affiliation(s)
- Cassia Fernanda Yano
- 1 Departamento de Genética e Evolução, Universidade Federal de São Carlos , São Carlos, Brazil
| | | | - Laureana Rebordinos
- 2 Laboratorio de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz , Cádiz, Spain
| | - Manuel Alejandro Merlo
- 2 Laboratorio de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz , Cádiz, Spain
| | - Thomas Liehr
- 3 Jena University Hospital, Friedrich Schiller University , Institute of Human Genetics, Jena, Germany
| | - Silvia Portela-Bens
- 2 Laboratorio de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz , Cádiz, Spain
| | - Marcelo de Bello Cioffi
- 1 Departamento de Genética e Evolução, Universidade Federal de São Carlos , São Carlos, Brazil
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25
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Paiz LM, Baumgärtner L, Graça WJD, Margarido VP, Pavanelli CS. Cytogenetics of Gymnogeophagus setequedas (Cichlidae: Geophaginae), with comments on its geographical distribution. NEOTROPICAL ICHTHYOLOGY 2017. [DOI: 10.1590/1982-0224-20160035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ABSTRACT We provide cytogenetic data for the threatened species Gymnogeophagus setequedas, and the first record of that species collected in the Iguaçu River, within the Iguaçu National Park’s area of environmental preservation, which is an unexpected occurrence for that species. We verified a diploid number of 2n = 48 chromosomes (4sm + 24st + 20a) and the presence of heterochromatin in centromeric and pericentromeric regions, which are conserved characters in the Geophagini. The multiple nucleolar organizer regions observed in G. setequedas are considered to be apomorphic characters in the Geophagini, whereas the simple 5S rDNA cistrons located interstitially on the long arm of subtelocentric chromosomes represent a plesiomorphic character. Because G. setequedas is a threatened species that occurs in lotic waters, we recommend the maintenance of undammed environments within its known area of distribution.
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Affiliation(s)
| | | | - Weferson J. da Graça
- Universidade Estadual de Maringá, Brazil; Universidade Estadual de Maringá, Brazil
| | - Vladimir P. Margarido
- Universidade Estadual de Maringá, Brazil; Universidade Estadual do Oeste do Paraná, Brazil
| | - Carla S. Pavanelli
- Universidade Estadual de Maringá, Brazil; Universidade Estadual de Maringá, Brazil
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26
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Gouveia JG, Wolf IR, de Moraes-Manécolo VPO, Bardella VB, Ferracin LM, Giuliano-Caetano L, da Rosa R, Dias AL. Isolation and characterization of 5S rDNA sequences in catfishes genome (Heptapteridae and Pseudopimelodidae): perspectives for rDNA studies in fish by C 0t method. Cytotechnology 2016; 68:2711-2720. [PMID: 27344147 PMCID: PMC5101342 DOI: 10.1007/s10616-016-9996-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 06/10/2016] [Indexed: 10/21/2022] Open
Abstract
Sequences of 5S ribosomal RNA (rRNA) are extensively used in fish cytogenomic studies, once they have a flexible organization at the chromosomal level, showing inter- and intra-specific variation in number and position in karyotypes. Sequences from the genome of Imparfinis schubarti (Heptapteridae) were isolated, aiming to understand the organization of 5S rDNA families in the fish genome. The isolation of 5S rDNA from the genome of I. schubarti was carried out by reassociation kinetics (C0t) and PCR amplification. The obtained sequences were cloned for the construction of a micro-library. The obtained clones were sequenced and hybridized in I. schubarti and Microglanis cottoides (Pseudopimelodidae) for chromosome mapping. An analysis of the sequence alignments with other fish groups was accomplished. Both methods were effective when using 5S rDNA for hybridization in I. schubarti genome. However, the C0t method enabled the use of a complete 5S rRNA gene, which was also successful in the hybridization of M. cottoides. Nevertheless, this gene was obtained only partially by PCR. The hybridization results and sequence analyses showed that intact 5S regions are more appropriate for the probe operation, due to conserved structure and motifs. This study contributes to a better understanding of the organization of multigene families in catfish's genomes.
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Affiliation(s)
- Juceli Gonzalez Gouveia
- Departamento de Biologia Geral, Centro de Ciências Biológicas, CCB, Universidade Estadual de Londrina, P.O Box 6001, Londrina, Paraná, CEP 86051-970, Brazil
| | - Ivan Rodrigo Wolf
- Departamento de Biologia Geral, Centro de Ciências Biológicas, CCB, Universidade Estadual de Londrina, P.O Box 6001, Londrina, Paraná, CEP 86051-970, Brazil
| | | | - Vanessa Belline Bardella
- Departamento de Biologia Geral, Centro de Ciências Biológicas, CCB, Universidade Estadual de Londrina, P.O Box 6001, Londrina, Paraná, CEP 86051-970, Brazil
| | - Lara Munique Ferracin
- Departamento de Biologia Geral, Centro de Ciências Biológicas, CCB, Universidade Estadual de Londrina, P.O Box 6001, Londrina, Paraná, CEP 86051-970, Brazil
| | - Lucia Giuliano-Caetano
- Departamento de Biologia Geral, Centro de Ciências Biológicas, CCB, Universidade Estadual de Londrina, P.O Box 6001, Londrina, Paraná, CEP 86051-970, Brazil
| | - Renata da Rosa
- Departamento de Biologia Geral, Centro de Ciências Biológicas, CCB, Universidade Estadual de Londrina, P.O Box 6001, Londrina, Paraná, CEP 86051-970, Brazil
| | - Ana Lúcia Dias
- Departamento de Biologia Geral, Centro de Ciências Biológicas, CCB, Universidade Estadual de Londrina, P.O Box 6001, Londrina, Paraná, CEP 86051-970, Brazil.
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27
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Evidence of birth-and-death evolution of 5S rRNA gene in Channa species (Teleostei, Perciformes). Genetica 2016; 144:723-732. [PMID: 27838803 DOI: 10.1007/s10709-016-9938-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 11/07/2016] [Indexed: 10/20/2022]
Abstract
In higher eukaryotes, minor rDNA family codes for 5S rRNA that is arranged in tandem arrays and comprises of a highly conserved 120 bp long coding sequence with a variable non-transcribed spacer (NTS). Initially the 5S rDNA repeats are considered to be evolved by the process of concerted evolution. But some recent reports, including teleost fishes suggested that evolution of 5S rDNA repeat does not fit into the concerted evolution model and evolution of 5S rDNA family may be explained by a birth-and-death evolution model. In order to study the mode of evolution of 5S rDNA repeats in Perciformes fish species, nucleotide sequence and molecular organization of five species of genus Channa were analyzed in the present study. Molecular analyses revealed several variants of 5S rDNA repeats (four types of NTS) and networks created by a neighbor net algorithm for each type of sequences (I, II, III and IV) did not show a clear clustering in species specific manner. The stable secondary structure is predicted and upstream and downstream conserved regulatory elements were characterized. Sequence analyses also shown the presence of two putative pseudogenes in Channa marulius. Present study supported that 5S rDNA repeats in genus Channa were evolved under the process of birth-and-death.
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28
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Unraveling the Sex Chromosome Heteromorphism of the Paradoxical Frog Pseudis tocantins. PLoS One 2016; 11:e0156176. [PMID: 27214234 PMCID: PMC4877019 DOI: 10.1371/journal.pone.0156176] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/10/2016] [Indexed: 11/25/2022] Open
Abstract
The paradoxical frog Pseudis tocantins is the only species in the Hylidae family with known heteromorphic Z and W sex chromosomes. The Z chromosome is metacentric and presents an interstitial nucleolar organizer region (NOR) on the long arm that is adjacent to a pericentromeric heterochromatic band. In contrast, the submetacentric W chromosome carries a pericentromeric NOR on the long arm, which is adjacent to a clearly evident heterochromatic band that is larger than the band found on the Z chromosome and justify the size difference observed between these chromosomes. Here, we provide evidence that the non-centromeric heterochromatic bands in Zq and Wq differ not only in size and location but also in composition, based on comparative genomic hybridization (CGH) and an analysis of the anuran PcP190 satellite DNA. The finding of PcP190 sequences in P. tocantins extends the presence of this satellite DNA, which was previously detected among Leptodactylidae and Hylodidae, suggesting that this family of repetitive DNA is even older than it was formerly considered. Seven groups of PcP190 sequences were recognized in the genome of P. tocantins. PcP190 probes mapped to the heterochromatic band in Wq, and a Southern blot analysis indicated the accumulation of PcP190 in the female genome of P. tocantins, which suggests the involvement of this satellite DNA in the evolution of the sex chromosomes of this species.
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29
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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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30
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Piscor D, Parise-Maltempi PP. Chromosomal mapping of H3 histone and 5S rRNA genes in eight species of Astyanax (Pisces, Characiformes) with different diploid numbers: syntenic conservation of repetitive genes. Genome 2016; 59:167-72. [DOI: 10.1139/gen-2015-0112] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genus Astyanax is widely distributed from the southern United States to northern Patagonia, Argentina. While cytogenetic studies have been performed for this genus, little is known about the histone gene families. The aim of this study was to examine the chromosomal relationships among the different species of Astyanax. The chromosomal locations of the 5S rRNA and H3 histone genes were determined in A. abramis, A. asuncionensis, A. altiparanae, A. bockmanni, A. eigenmanniorum, A. mexicanus (all 2n = 50), A. fasciatus (2n = 46), and A. schubarti (2n = 36). All eight species exhibited H3 histone clusters on two chromosome pairs. In six species (A. abramis, A. asuncionensis, A. altiparanae, A. bockmanni, A. eigenmanniorum, and A. fasciatus), syntenic clusters of H3 histone and 5S rDNA were observed on metacentric (m) or submetacentric (sm) chromosomes. In seven species, clusters of 5S rDNA sequences were located on one or two chromosome pairs. In A. mexicanus, 5S rDNA clusters were located on four chromosome pairs. This study demonstrates that H3 histone clusters are conserved on two chromosome pairs in the genus Astyanax, and specific chromosomal features may contribute to the genomic organization of the H3 histone and 5S rRNA genes.
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Affiliation(s)
- Diovani Piscor
- Instituto de Biociências, Departamento de Biologia, Laboratório de Citogenética, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Av. 24A, 1515, ZIP: 13506-900, Rio Claro, SP, Brazil
- Instituto de Biociências, Departamento de Biologia, Laboratório de Citogenética, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Av. 24A, 1515, ZIP: 13506-900, Rio Claro, SP, Brazil
| | - Patricia Pasquali Parise-Maltempi
- Instituto de Biociências, Departamento de Biologia, Laboratório de Citogenética, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Av. 24A, 1515, ZIP: 13506-900, Rio Claro, SP, Brazil
- Instituto de Biociências, Departamento de Biologia, Laboratório de Citogenética, Universidade Estadual Paulista “Júlio de Mesquita Filho” (UNESP), Av. 24A, 1515, ZIP: 13506-900, Rio Claro, SP, Brazil
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Oliveira MLMD, Utsunomia R, Pansonato-Alves JC, Scacchetti PC, Primo CC, Vicari MR, Artoni RF, Centofante L, Moreira-Filho O, Oliveira C, Foresti F. Microstructural chromosome reorganization in the genus Trichomycterus (Siluriformes: Trichomycteridae). NEOTROPICAL ICHTHYOLOGY 2016. [DOI: 10.1590/1982-0224-20150084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Trichomycterus is a specious fish genus within Trichomycterinae and displays remarkable karyotype diversity. However, knowledge about their genomic structure and location of repetitive sequence is still limited. In order to better understand the karyotype diversification, we analyzed nine species of Trichomycterus using classical and molecular cytogenetic techniques. Results revealed a conserved diploid chromosome number of 2n=54 chromosomes in all analyzed species, although remarkable differences on the constitutive heterochromatin distribution were observed. In addition, while the 18S rDNA showed a conserved distribution pattern, the 5S rDNA sites showed a quite diverse location considering the analyzed species. Remarkably, both ribosomal genes were co-located in all species, except in T . iheringi , suggesting that co-localization is probably an ancestral condition in Trichomycterus . Finally, three analyzed species showed heterochromatic B chromosomes, reinforcing the intense genomic reorganization occurring in Trichomycterus . Our results showed that chromosomal variations are not restricted to differences in karyotype formula as previously proposed, but also to modifications on the microstructural level of resolution.
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32
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García-Souto D, Troncoso T, Pérez M, Pasantes JJ. Molecular Cytogenetic Analysis of the European Hake Merluccius merluccius (Merlucciidae, Gadiformes): U1 and U2 snRNA Gene Clusters Map to the Same Location. PLoS One 2015; 10:e0146150. [PMID: 26716701 PMCID: PMC4696792 DOI: 10.1371/journal.pone.0146150] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 12/13/2015] [Indexed: 01/25/2023] Open
Abstract
The European hake (Merluccius merluccius) is a highly valuable and intensely fished species in which a long-term alive stock has been established in captivity for aquaculture purposes. Due to their huge economic importance, genetic studies on hakes were mostly focused on phylogenetic and phylogeographic aspects; however chromosome numbers are still not described for any of the fifteen species in the genus Merluccius. In this work we report a chromosome number of 2n = 42 and a karyotype composed of three meta/submetacentric and 18 subtelo/telocentric chromosome pairs. Telomeric sequences appear exclusively at both ends of every single chromosome. Concerning rRNA genes, this species show a single 45S rDNA cluster at an intercalary location on the long arm of subtelocentric chromosome pair 12; the single 5S rDNA cluster is also intercalary to the long arm of chromosome pair 4. While U2 snRNA gene clusters map to a single subcentromeric position on chromosome pair 13, U1 snRNA gene clusters seem to appear on almost all chromosome pairs, but showing bigger clusters on pairs 5, 13, 16, 17 and 19. The brightest signals on pair 13 are coincident with the single U2 snRNA gene cluster signals. Therefore, the use of these probes allows the unequivocal identification of at least 7 of the chromosome pairs that compose the karyotype of Merluccius merluccius thus opening the way to integrate molecular genetics and cytological data on the study of the genome of this important species.
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Affiliation(s)
- Daniel García-Souto
- Departamento de Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, Vigo, Spain
| | - Tomás Troncoso
- Departamento de Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, Vigo, Spain
- Grupo de Acuicultura Marina, Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, Vigo, Spain
| | - Montse Pérez
- Grupo de Acuicultura Marina, Centro Oceanográfico de Vigo, Instituto Español de Oceanografía, Vigo, Spain
| | - Juan José Pasantes
- Departamento de Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, Vigo, Spain
- * E-mail:
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33
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Sember A, Bohlen J, Šlechtová V, Altmanová M, Symonová R, Ráb P. Karyotype differentiation in 19 species of river loach fishes (Nemacheilidae, Teleostei): extensive variability associated with rDNA and heterochromatin distribution and its phylogenetic and ecological interpretation. BMC Evol Biol 2015; 15:251. [PMID: 26573692 PMCID: PMC4647339 DOI: 10.1186/s12862-015-0532-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 11/04/2015] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Loaches of the family Nemacheilidae are one of the most speciose elements of Palearctic freshwater ichthyofauna and have undergone rapid ecological adaptations and colonizations. Their cytotaxonomy is largely unexplored; with the impact of cytogenetical changes on this evolutionary diversification still unknown. An extensive cytogenetical survey was performed in 19 nemacheilid species using both conventional (Giemsa staining, C- banding, Ag- and Chromomycin A3/DAPI stainings) and molecular (fluorescence in situ hybridization with 5S rDNA, 45S rDNA, and telomeric (TTAGGG)n probes) methods. A phylogenetic tree of the analysed specimens was constructed based on one mitochondrial (cytochrome b) and two nuclear (RAG1, IRBP) genes. RESULTS Seventeen species showed karyotypes composed of 2n = 50 chromosomes but differentiated by fundamental chromosome number (NF = 68-90). Nemachilichthys ruppelli (2n = 38) and Schistura notostigma (2n = 44-48) displayed reduced 2n with an elevated number of large metacentric chromosomes. Only Schistura fasciolata showed morphologically differentiated sex chromosomes with a multiple system of the XY1Y2 type. Chromomycin A3 (CMA3)- fluorescence revealed interspecific heterogeneity in the distribution of GC-rich heterochromatin including its otherwise very rare association with 5S rDNA sites. The 45S rDNA sites were mostly located on a single chromosome pair contrasting markedly with a pattern of two (Barbatula barbatula, Nemacheilus binotatus, N. ruppelli) to 20 sites (Physoschistura sp.) of 5S rDNA. The cytogenetic changes did not follow the phylogenetic relationships between the samples. A high number of 5S rDNA sites was present in species with small effective population sizes. CONCLUSION Despite a prevailing conservatism of 2n, Nemacheilidae exhibited a remarkable cytogenetic variability on microstructural level. We suggest an important role for pericentric inversions, tandem and centric fusions in nemacheilid karyotype differentiation. Short repetitive sequences, genetic drift, founder effect, as well as the involvement of transposable elements in the dispersion of ribosomal DNA sites, might also have played a role in evolutionary processes such as reproductive isolation. These remarkable dynamics of their genomes qualify river loaches as a model for the study of the cytogenetic background of major evolutionary processes such as radiation, endemism and colonization of a wide range of habitats.
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Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 128 44, Prague 2, Czech Republic.
| | - Jörg Bohlen
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
| | - Vendula Šlechtová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
| | - Marie Altmanová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
- Department of Ecology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44, Prague 2, Czech Republic.
| | - Radka Symonová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
- Research Institute for Limnology, University of Innsbruck, Mondseestraße 9, A-5310, Mondsee, Austria.
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic.
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de Sene VF, Pansonato-Alves JC, Ferreira DC, Utsunomia R, Oliveira C, Foresti F. Mapping of the Retrotransposable Elements Rex1 and Rex3 in Chromosomes of Eigenmannia (Teleostei, Gymnotiformes, Sternopygidae). Cytogenet Genome Res 2015; 146:319-24. [DOI: 10.1159/000441465] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2015] [Indexed: 11/19/2022] Open
Abstract
Transposable elements constitute a remarkable fraction of the eukaryote genome and show particular capacity to move and insert in specific regions of the genome. This study identified the retrotransposable elements Rex1 and Rex3 in the genomes of 6 cytotypes of Eigenmannia. The sequences were isolated by PCR, sequenced and physically mapped in the chromosomes of these cytotypes, aiming to investigate the organization and distribution of these elements in this fish group, mainly in the sex chromosomes. The FISH physical mapping revealed that both Rex1 and Rex3 elements are dispersed in small clusters throughout the chromosomes of all cytotypes analyzed. However, conspicuous blocks occur in several samples, including an accentuated accumulation of the Rex3 element in X1 and X2 chromosomes of Eigenmannia sp. 2 and in the X chromosome of E. virescens. The accumulations are coincident with heterochromatin-rich regions, suggesting that Rex3 played a role in the differentiation process of the sex chromosomes.
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Roa F, Guerra M. Non-Random Distribution of 5S rDNA Sites and Its Association with 45S rDNA in Plant Chromosomes. Cytogenet Genome Res 2015; 146:243-9. [PMID: 26489031 DOI: 10.1159/000440930] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2015] [Indexed: 11/19/2022] Open
Abstract
5S and 45S rDNA sites are the best mapped chromosome regions in eukaryotic chromosomes. In this work, a database was built gathering information about the position and number of 5S rDNA sites in 784 plant species, aiming to identify patterns of distribution along the chromosomes and its correlation with the position of 45S rDNA sites. Data revealed that in most karyotypes (54.5%, including polyploids) two 5S rDNA sites (a single pair) are present, with 58.7% of all sites occurring in the short arm, mainly in the proximal region. In karyotypes of angiosperms with only 1 pair of sites (single sites) they are mostly found in the proximal region (52.0%), whereas in karyotypes with multiple sites the location varies according to the average chromosome size. Karyotypes with multiple sites and small chromosomes (<3 µm) often display proximal sites, while medium-sized (between 3 and 6 µm) and large chromosomes (>6 µm) more commonly show terminal or interstitial sites. In species with holokinetic chromosomes, the modal value of sites per karyotype was also 2, but they were found mainly in a terminal position. Adjacent 5S and 45S rDNA sites were often found in the short arm, reflecting the preferential distribution of both sites in this arm. The high frequency of genera with at least 1 species with adjacent 5S and 45S sites reveals that this association appeared several times during angiosperm evolution, but it has been maintained only rarely as the dominant array in plant genera.
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Baumgärtner L, Paiz LM, Zawadzki CH, Margarido VP, Castro ALDBP. Heterochromatin polymorphism and physical mapping of 5S and 18S ribosomal DNA in four populations of Hypostomus strigaticeps (Regan, 1907) from the Paraná River basin, Brazil: evolutionary and environmental correlation. Zebrafish 2015; 11:479-87. [PMID: 25237984 DOI: 10.1089/zeb.2014.1028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A cytogenetic analysis was performed on four populations of Hypostomus strigaticeps from the Paraná River basin, Brazil. Two populations were collected from the large channel river at the Itaipu reservoir area and the other two were from the upper stretches of tributaries of the Paraná River. All populations showed 2n=72 chromosomes (12m+12sm+18st+30a), intra- and interpopulation 18S rDNA site polymorphisms (two to three acrocentric chromosome pairs), and multiple 5S rDNA sites in three chromosome pairs (4, 21, and 28). C-banding revealed heterochromatin located in the centromere and pericentromere regions of most chromosome; however, large heterochromatic blocks (CMA3(-)/DAPI(+)) on the long arm of acrocentric chromosomes identified intra- and interpopulation polymorphism. The amount and distribution of heterochromatin seem to be correlated to biogeographical characteristics of H. strigaticeps along the Paraná River. Morphometric results also showed diversity among the populations, suggesting phenotypic plasticity of this species. Evolutionary, taxonomy, and biogeographical approaches with regard to H. strigaticeps and interrelationships in Hypostomus are discussed.
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Affiliation(s)
- Lucas Baumgärtner
- 1 Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá , Maringá, Brazil
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Coutinho-Sanches N, Dergam JA. Cytogenetic and Molecular Data Suggest Deuterodon pedri Eigenmann, 1907 (Teleostei: Characidae) Is a Member of an Ancient Coastal Group. Zebrafish 2015; 12:357-65. [PMID: 26267614 DOI: 10.1089/zeb.2014.1068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The genus Deuterodon has been taxonomically recently redefined. Seven of its species have been included in this genus, whereas three others are regarded as Incertae Sedis in Characidae. One of latter is Deuterodon pedri, an endemic species from Santo Antônio River in Minas Gerais. Cytogenetic and molecular data on 21 specimens of D. pedri allowed to reevaluate the phylogenetic position of this taxon. The specimens showed karyotypic formula 12m+12sm+20st+6a, low heterochromatin content, nucleolar organizer regions present in two chromosome pairs, and 10 and 2 labeled regions by fluorescence in situ hybridization with 18S and 5S probes respectively, a karyotype similar to Deuterodon stigmaturus. The phylogenetic tree generated by a cytochrome oxidase subunit I fragment revealed that D. pedri and Deuterodon singularis are closely related and are the sister-group of Deuterodon parahybae, Deuterodon iguape, Astyanax giton, Astyanax intermedius, Astyanax ribeirae, Astyanax scabripinnis, and Probolodus heterostomus. The same arrangement was partially recovered with the nuclear gene RAG2. Our data indicate the genus Deuterodon is not monophyletic and that it is closely related to other species that occur in Brazil coastal basins.
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Affiliation(s)
- Natália Coutinho-Sanches
- Laboratório de Sistemática Molecular "Beagle," Departamento de Biologia Animal, Universidade Federal de Viçosa , Viçosa, Minas Gerais, Brazil
| | - Jorge Abdala Dergam
- Laboratório de Sistemática Molecular "Beagle," Departamento de Biologia Animal, Universidade Federal de Viçosa , Viçosa, Minas Gerais, Brazil
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Shapoval NA, Lukhtanov VA. Intragenomic variations of multicopy ITS2 marker in Agrodiaetus blue butterflies (Lepidoptera, Lycaenidae). COMPARATIVE CYTOGENETICS 2015; 9:483-97. [PMID: 26753069 PMCID: PMC4698565 DOI: 10.3897/compcytogen.v9i4.5429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 07/20/2015] [Indexed: 05/31/2023]
Abstract
The eukaryotic ribosomal DNA cluster consists of multiple copies of three genes, 18S, 5. 8S and 28S rRNAs, separated by multiple copies of two internal transcribed spacers, ITS1 and ITS2. It is an important, frequently used marker in both molecular cytogenetic and molecular phylogenetic studies. Despite this, little is known about intragenomic variations within the copies of eukaryotic ribosomal DNA genes and spacers. Here we present data on intraindividual variations of ITS2 spacer in three species of Agrodiaetus Hübner, 1822 blue butterflies revealed by cloning technique. We demonstrate that a distinctly different intragenomic ITS2 pattern exists for every individual analysed. ITS2 sequences of these species show significant intragenomic variation (up to 3.68% divergence), setting them apart from each other on inferred phylogenetic tree. This variation is enough to obscure phylogenetic relationships at the species level.
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Affiliation(s)
- Nazar A. Shapoval
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199034, Russia
- Department of Entomology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg 199034, Russia
| | - Vladimir A. Lukhtanov
- Department of Karyosystematics, Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg 199034, Russia
- Department of Entomology, Faculty of Biology, St. Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg 199034, Russia
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Nachtigall PG, Dias MC, Carvalho RF, Martins C, Pinhal D. MicroRNA-499 expression distinctively correlates to target genes sox6 and rod1 profiles to resolve the skeletal muscle phenotype in Nile tilapia. PLoS One 2015; 10:e0119804. [PMID: 25793727 PMCID: PMC4368118 DOI: 10.1371/journal.pone.0119804] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 02/02/2015] [Indexed: 11/22/2022] Open
Abstract
A class of small non-coding RNAs, the microRNAs (miRNAs), has been shown to be essential for the regulation of specific cell pathways, including skeletal muscle development, maintenance and homeostasis in vertebrates. However, the relative contribution of miRNAs for determining the red and white muscle cell phenotypes is far from being fully comprehended. To better characterize the role of miRNA in skeletal muscle cell biology, we investigated muscle-specific miRNA (myomiR) signatures in Nile tilapia fish. Quantitative (RT-qPCR) and spatial (FISH) expression analyses revealed a highly differential expression (forty-four-fold) of miR-499 in red skeletal muscle compared to white skeletal muscle, whereas the remaining known myomiRs were equally expressed in both muscle cell types. Detailed examination of the miR-499 targets through bioinformatics led us to the sox6 and rod1 genes, which had low expression in red muscle cells according to RT-qPCR, FISH, and protein immunofluorescence profiling experiments. Interestingly, we verified that the high expression of miR-499 perfectly correlates with a low expression of sox6 and rod1 target genes, as verified by a distinctive predominance of mRNA destabilization and protein translational decay to these genes, respectively. Through a genome-wide comparative analysis of SOX6 and ROD1 protein domains and through an in silico gene regulatory network, we also demonstrate that both proteins are essentially similar in vertebrate genomes, suggesting their gene regulatory network may also be widely conserved. Overall, our data shed light on the potential regulation of targets by miR-499 associated with the slow-twitch muscle fiber type phenotype. Additionally the results provide novel insights into the evolutionary dynamics of miRNA and target genes enrolled in a putative constrained molecular pathway in the skeletal muscle cells of vertebrates.
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Affiliation(s)
- Pedro G. Nachtigall
- Department of Genetics, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-970, Brazil
| | - Marcos C. Dias
- Department of Morphology, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-970, Brazil
- Health Sciences Institute, Federal University of Mato Grosso (UFMT), Sinop, Mato Grosso, 78550-000, Brazil
| | - Robson F. Carvalho
- Department of Morphology, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-970, Brazil
| | - Cesar Martins
- Department of Morphology, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-970, Brazil
| | - Danillo Pinhal
- Department of Genetics, Institute of Biosciences, Sao Paulo State University (UNESP), Botucatu, Sao Paulo, 18618-970, Brazil
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Schneider CH, Gross MC, Terencio ML, de Tavares ÉSGM, Martins C, Feldberg E. Chromosomal distribution of microsatellite repeats in Amazon cichlids genome (Pisces, Cichlidae). COMPARATIVE CYTOGENETICS 2015; 9:595-605. [PMID: 26753076 PMCID: PMC4698573 DOI: 10.3897/compcytogen.v9i4.5582] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/21/2014] [Indexed: 05/10/2023]
Abstract
Fish of the family Cichlidae are recognized as an excellent model for evolutionary studies because of their morphological and behavioral adaptations to a wide diversity of explored ecological niches. In addition, the family has a dynamic genome with variable structure, composition and karyotype organization. Microsatellites represent the most dynamic genomic component and a better understanding of their organization may help clarify the role of repetitive DNA elements in the mechanisms of chromosomal evolution. Thus, in this study, microsatellite sequences were mapped in the chromosomes of Cichla monoculus Agassiz, 1831, Pterophyllum scalare Schultze, 1823, and Symphysodon discus Heckel, 1840. Four microsatellites demonstrated positive results in the genome of Cichla monoculus and Symphysodon discus, and five demonstrated positive results in the genome of Pterophyllum scalare. In most cases, the microsatellite was dispersed in the chromosome with conspicuous markings in the centromeric or telomeric regions, which suggests that sequences contribute to chromosome structure and may have played a role in the evolution of this fish family. The comparative genome mapping data presented here provide novel information on the structure and organization of the repetitive DNA region of the cichlid genome and contribute to a better understanding of this fish family's genome.
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Affiliation(s)
- Carlos Henrique Schneider
- Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Departamento de Genética, Laboratório de Citogenômica Animal, Av. General Rodrigo Otávio, 3000, Japiim, Zip code 69077-000 Manaus, AM, Brazil
| | - Maria Claudia Gross
- Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Departamento de Genética, Laboratório de Citogenômica Animal, Av. General Rodrigo Otávio, 3000, Japiim, Zip code 69077-000 Manaus, AM, Brazil
| | - Maria Leandra Terencio
- Universidade Federal da Integração Latino Americana, Laboratório de Genética, Av. Tarquínio Joslin dos Santos, 1000, Jardim Universitário, Zip code 85857-190, Foz do Iguaçu, PR, Brazil
| | - Édika Sabrina Girão Mitozo de Tavares
- Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Departamento de Genética, Laboratório de Citogenômica Animal, Av. General Rodrigo Otávio, 3000, Japiim, Zip code 69077-000 Manaus, AM, Brazil
| | - Cesar Martins
- Universidade Estadual Paulista Júlio de Mesquita Filho – UNESP, Instituto de Biociências, Departamento de Morfologia, Laboratório Genômica Integrativa, Rubião Junior, Zip code 18618-000 Botucatu, SP, Brazil
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia, Laboratório de Genética Animal, Av. André Araújo, 2936 Zip Code 69077-000, Manaus, AM, Brazil
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Piscor D, Alves AL, Parise-Maltempi PP. Chromosomal microstructure diversity in three Astyanax (Characiformes, Characidae) species: comparative analysis of the chromosomal locations of the 18S and 5S rDNAs. Zebrafish 2014; 12:81-90. [PMID: 25549064 DOI: 10.1089/zeb.2014.1036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The species of genus Astyanax is widely distributed in freshwater neotropical zones. Astyanax is considered to be taxonomically confused, similar to other genera placed incertae sedis in Characidae. The cytogenetics of this genus is well characterized; species vary widely in diploid number, from 2n=36 chromosomes in Astyanax schubarti to 2n=50 for most species studied. The size, number, and position of different cytological markers vary among species and populations of Astyanax. We analyzed the karyotypes of individuals from three Astyanax species (Astyanax abramis, Astyanax altiparanae, and Astyanax eigenmanniorum) from populations not previously analyzed. We describe variations in several cytogenetic markers and the karyotypic relationships between them, specifically focusing on the characteristics of the conserved and divergent locations of the ribosomal genes. Our data are useful for establishing relationships between species and for investigating the karyotype evolution within the genus.
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Affiliation(s)
- Diovani Piscor
- 1 Laboratório de Citogenética, Departamento de Biologia, Instituto de Biociências, Universidade Estadual Paulista "Júlio de Mesquita Filho" (UNESP) , Rio Claro, Sao Paulo, Brazil
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Physical mapping of the 5S and 18S rDNA in ten species of Hypostomus Lacépède 1803 (Siluriformes: Loricariidae): evolutionary tendencies in the genus. ScientificWorldJournal 2014; 2014:943825. [PMID: 25405240 PMCID: PMC4227443 DOI: 10.1155/2014/943825] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/24/2014] [Indexed: 11/29/2022] Open
Abstract
Hypostomus is a diverse group with unclear aspects regarding its biology, including the mechanisms that led to chromosome diversification within the group. Fluorescence in situ hybridization (FISH) with 5S and 18S rDNA probes was performed on ten Hypostomini species. Hypostomus faveolus, H. cochliodon, H. albopunctatus, H. aff. paulinus, and H. topavae had only one chromosome pair with 18S rDNA sites, while H. ancistroides, H. commersoni, H. hermanni, H. regani, and H. strigaticeps had multiple 18S rDNA sites. Regarding the 5S rDNA genes, H. ancistroides, H. regani, H. albopunctatus, H. aff. paulinus, and H. topavae had 5S rDNA sites on only one chromosome pair and H. faveolus, H. cochliodon, H. commersoni, H. hermanni, and H. strigaticeps had multiple 5S rDNA sites. Most species had 18S rDNA sites in the telomeric region of the chromosomes. All species but H. cochliodon had 5S rDNA in the centromeric/pericentromeric region of one metacentric pair. Obtained results are discussed based on existent phylogenies for the genus, with comments on possible dispersion mechanisms to justify the variability of the rDNA sites in Hypostomus.
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Spoz A, Boron A, Porycka K, Karolewska M, Ito D, Abe S, Kirtiklis L, Juchno D. Molecular cytogenetic analysis of the crucian carp, Carassius carassius (Linnaeus, 1758) (Teleostei, Cyprinidae), using chromosome staining and fluorescence in situ hybridisation with rDNA probes. COMPARATIVE CYTOGENETICS 2014; 8:233-48. [PMID: 25349674 PMCID: PMC4205492 DOI: 10.3897/compcytogen.v8i3.7718] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 07/28/2014] [Indexed: 05/13/2023]
Abstract
The crucian carp Carassius carassius (Linnaeus, 1758) is a species with restricted and decreasing distribution in Europe. Six males and six females of the species from the Baltic Sea basin in Poland were examined to show sequentially CMA3/AgNO3 staining pattern, DAPI staining, and, for the first time in literature, molecular cytogenetic analysis using double-colour fluorescence in situ hybridisation (FISH) with 28S and 5S rDNA probes. The karyotype consisted of 20 m, 36 sm and 44 sta chromosomes, NF=156. The AgNO3 stained NORs were most frequently located terminally in the short arms of two sm and two sta elements, and CMA3-positive sites were also observed suggesting abundant GC-rich repetitive DNA in the regions. Other CMA3-positive sites in the short arms of six to ten sm and sta chromosomes were detected. The results based on 28S rDNA FISH confirmed the location of rDNA sites. DAPI-negative staining of NORs suggested the scarcity of AT-rich DNA in the regions. FISH with 5S rDNA probe revealed 8-14 loci (ten and 12 in respectively 49 and 29% of metaphases). They were located in two sm and eight to ten sta chromosomes and six of them were larger than others. Simultaneously, mapping of the two rDNA families on the chromosomes of C. carassius revealed that both 28S and 5S rDNA probes were located in different chromosomes. Molecular cytogenetic data of C. carassius presented here for the first time give an important insight into the structure of chromosomes of this polyploid and declining species and may be useful in its systematics.
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Affiliation(s)
- Aneta Spoz
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego Str. 5, 10-718 Olsztyn, Poland
| | - Alicja Boron
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego Str. 5, 10-718 Olsztyn, Poland
| | - Katarzyna Porycka
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego Str. 5, 10-718 Olsztyn, Poland
| | - Monika Karolewska
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego Str. 5, 10-718 Olsztyn, Poland
| | - Daisuke Ito
- Instituto Gulbenkian de Ciência, Rua da Quinta Grade, 6, 2780-156, Oeiras, Portugal
| | - Syuiti Abe
- Sanriku Fisheries Research Center, Department of Revitalization for Sanriku-region, Iwate University, 3-75-1, Heita, Kamaishi 026-0001, Iwate, Japan
| | - Lech Kirtiklis
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego Str. 5, 10-718 Olsztyn, Poland
| | - Dorota Juchno
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, M. Oczapowskiego Str. 5, 10-718 Olsztyn, Poland
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Porto FE, de Rossi Vieira MM, Barbosa LM, Borin-Carvalho LA, Vicari MR, de Brito Portela-Castro AL, Martins-Santos IC. Chromosomal Polymorphism in Rineloricaria Lanceolata Günther, 1868 (Loricariidae: Loricariinae) of the Paraguay Basin (Mato Grosso do Sul, Brazil): Evidence of Fusions and Their Consequences in the Population. Zebrafish 2014; 11:318-24. [DOI: 10.1089/zeb.2014.0996] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Fernanda Errero Porto
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, Brazil
| | | | - Ligia Magrinelli Barbosa
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, Brazil
| | | | - Marcelo Ricardo Vicari
- Setor de Ciências Biológicas e da Saúde/Debiogem, Universidade Estadual de Ponta Grossa, Ponta Grossa, Brazil
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Kuznetsova IS, Thevasagayam NM, Sridatta PSR, Komissarov AS, Saju JM, Ngoh SY, Jiang J, Shen X, Orbán L. Primary analysis of repeat elements of the Asian seabass (Lates calcarifer) transcriptome and genome. Front Genet 2014; 5:223. [PMID: 25120555 PMCID: PMC4110674 DOI: 10.3389/fgene.2014.00223] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 06/27/2014] [Indexed: 02/05/2023] Open
Abstract
As part of our Asian seabass genome project, we are generating an inventory of repeat elements in the genome and transcriptome. The karyotype showed a diploid number of 2n = 24 chromosomes with a variable number of B-chromosomes. The transcriptome and genome of Asian seabass were searched for repetitive elements with experimental and bioinformatics tools. Six different types of repeats constituting 8–14% of the genome were characterized. Repetitive elements were clustered in the pericentromeric heterochromatin of all chromosomes, but some of them were preferentially accumulated in pretelomeric and pericentromeric regions of several chromosomes pairs and have chromosomes specific arrangement. From the dispersed class of fish-specific non-LTR retrotransposon elements Rex1 and MAUI-like repeats were analyzed. They were wide-spread both in the genome and transcriptome, accumulated on the pericentromeric and peritelomeric areas of all chromosomes. Every analyzed repeat was represented in the Asian seabass transcriptome, some showed differential expression between the gonads. The other group of repeats analyzed belongs to the rRNA multigene family. FISH signal for 5S rDNA was located on a single pair of chromosomes, whereas that for 18S rDNA was found on two pairs. A BAC-derived contig containing rDNA was sequenced and assembled into a scaffold containing incomplete fragments of 18S rDNA. Their assembly and chromosomal position revealed that this part of Asian seabass genome is extremely rich in repeats containing evolutionarily conserved and novel sequences. In summary, transcriptome assemblies and cDNA data are suitable for the identification of repetitive DNA from unknown genomes and for comparative investigation of conserved elements between teleosts and other vertebrates.
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Affiliation(s)
- Inna S Kuznetsova
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, The National University of Singapore Singapore, Republic of Singapore ; Institute of Cytology of the Russian Academy of Sciences St-Petersburg, Russia
| | - Natascha M Thevasagayam
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, The National University of Singapore Singapore, Republic of Singapore
| | - Prakki S R Sridatta
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, The National University of Singapore Singapore, Republic of Singapore
| | - Aleksey S Komissarov
- Institute of Cytology of the Russian Academy of Sciences St-Petersburg, Russia ; Theodosius Dobzhansky Center for Genome Bioinformatics, St Petersburg State University St Petersburg, Russia
| | - Jolly M Saju
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, The National University of Singapore Singapore, Republic of Singapore
| | - Si Y Ngoh
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, The National University of Singapore Singapore, Republic of Singapore ; School of Biological Sciences, Nanyang Technological University Singapore, Republic of Singapore
| | - Junhui Jiang
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, The National University of Singapore Singapore, Republic of Singapore ; Agri-Food and Veterinary Authority of Singapore Singapore, Republic of Singapore
| | - Xueyan Shen
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, The National University of Singapore Singapore, Republic of Singapore
| | - László Orbán
- Reproductive Genomics Group, Strategic Research Program, Temasek Life Sciences Laboratory, The National University of Singapore Singapore, Republic of Singapore ; Department of Animal Sciences and Animal Husbandry, Georgikon Faculty, University of Pannonia Keszthely, Hungary ; Department of Biological Sciences, National University of Singapore Singapore, Republic of Singapore
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Molecular cytogenetic study of the European bitterling Rhodeus amarus (Teleostei: Cyprinidae: Acheilognathinae). Genetica 2014; 142:141-8. [PMID: 24677088 PMCID: PMC4000624 DOI: 10.1007/s10709-014-9761-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Accepted: 03/21/2014] [Indexed: 11/06/2022]
Abstract
The European bitterlings (Rhodeus amarus) from the Eastern locations were cytogenetically examined by conventional and molecular techniques. All analyzed individuals presented invariably the same chromosomal constitution of 2n = 48, with 8 metacentrics + 20 submetacentrics + 20 subtelo-acrocentrics and C-banding positive heterochromatin at the pericentromeric regions in most of the chromosomes. Moreover, some of the chromosomes had short arms entirely built with heterochromatin. GC-rich Ag-NORs (nucleolus organizer regions) were located at the short arms of two submetacentric chromosomes, and the length polymorphism of these regions was found. Multiple location of 28S rDNA sequences with fluorescence in situ hybridization signals was observed on the long and/or short arms of three submetacentric chromosomes including NOR regions and short arms of three to five acrocentric chromosomes in the studied fish. 5S rDNA sites were found on the short arms of two subtelocentric chromosomes, and telomeric repeats were localized at the ends of all chromosomes. Provided results have expanded our knowledge concerning genetic characteristics of the European bitterlings that may be profitable in the conservation programs of this endangered species.
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Pucci MB, Barbosa P, Nogaroto V, Almeida MC, Artoni RF, Pansonato-Alves JC, Foresti F, Moreira-Filho O, Vicari MR. Population differentiation and speciation in the genusCharacidium(Characiformes: Crenuchidae): effects of reproductive and chromosomal barriers. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12218] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Marcela Baer Pucci
- Departamento de Biologia Estrutural, Molecular e Genética; Universidade Estadual de Ponta Grossa; Av. Carlos Cavalcanti, 4748 Ponta Grossa-PR 84030-900 Brazil
| | - Patrícia Barbosa
- Departamento de Biologia Estrutural, Molecular e Genética; Universidade Estadual de Ponta Grossa; Av. Carlos Cavalcanti, 4748 Ponta Grossa-PR 84030-900 Brazil
| | - Viviane Nogaroto
- Departamento de Biologia Estrutural, Molecular e Genética; Universidade Estadual de Ponta Grossa; Av. Carlos Cavalcanti, 4748 Ponta Grossa-PR 84030-900 Brazil
| | - Mara Cristina Almeida
- Departamento de Biologia Estrutural, Molecular e Genética; Universidade Estadual de Ponta Grossa; Av. Carlos Cavalcanti, 4748 Ponta Grossa-PR 84030-900 Brazil
| | - Roberto Ferreira Artoni
- Departamento de Biologia Estrutural, Molecular e Genética; Universidade Estadual de Ponta Grossa; Av. Carlos Cavalcanti, 4748 Ponta Grossa-PR 84030-900 Brazil
| | - José Carlos Pansonato-Alves
- Departamento de Morfologia; Universidade Estadual Paulista; Distrito de Rubião Junior, s/n Botucatu-SP 18618-970 Brazil
| | - Fausto Foresti
- Departamento de Morfologia; Universidade Estadual Paulista; Distrito de Rubião Junior, s/n Botucatu-SP 18618-970 Brazil
| | - Orlando Moreira-Filho
- Departamento de Genética e Evolução; Universidade Federal de São Carlos; Rodovia Washington Luís, Km 235 São Carlos-SP 13565-905 Brazil
| | - Marcelo Ricardo Vicari
- Departamento de Biologia Estrutural, Molecular e Genética; Universidade Estadual de Ponta Grossa; Av. Carlos Cavalcanti, 4748 Ponta Grossa-PR 84030-900 Brazil
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Extensive chromosome conservatism in Atlantic butterflyfishes, genus Chaetodon Linnaeus, 1758: Implications for the high hybridization success. ZOOL ANZ 2013. [DOI: 10.1016/j.jcz.2013.10.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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49
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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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50
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Tenório RCCDO, Vitorino CDA, Souza IL, Oliveira C, Venere PC. Comparative cytogenetics in Astyanax (Characiformes: Characidae) with focus on the cytotaxonomy of the group. NEOTROPICAL ICHTHYOLOGY 2013. [DOI: 10.1590/s1679-62252013000300008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Astyanax is a diverse group of Neotropical fishes, whose different forms occupy different environments. This great diversity is also reflected on cytogenetic aspects and molecular markers, which have repeatedly been demonstrated by cytogenetic studies. In order to characterize the karyotype of species of this genus, six species were studied: Astyanax altiparanae, A.argyrimarginatus, A. elachylepis, A. xavante, and two new species provisionally called Astyanax sp. and A. aff. bimaculatus. A detailed cytogenetic study based on conventional staining with Giemsa, AgNORs, C-banding, base-specific fluorochromes, and FISH using ribosomal genes 18S and 5S was conducted, aiming to understand some of the chromosomal mechanisms associated with the high diversification that characterizes this group and culminated with the establishment of these species. The results showed 2n = 50 chromosomes for five species and a karyotype with 52 chromosomes in Astyanax sp. Small variations in the macrostructure of the karyotypes were identified, which were quite relevant when analyzed by classical banding, fluorochromes, and FISH methods. These differences among Astyanax spp. (2n = 50) are largely due to changes in the amount and types of heterochromatic blocks. Astyanax sp (2n = 52), in addition to variations due to heterochromatic blocks, has its origin possibly by events of centric fission in a pair of chromosomes followed by minor rearrangements.These results show an interesting karyotypic diversity in Astyanax and indicate the need of a review of the group referred as A. aff. bimaculatus and the description of Astyanax sp., including the possibility of inclusion of this unit in another genus.
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