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Amorim KDJ, Costa GWWF, Motta-Neto CC, Soares RX, Borges AT, Benetti DD, Cioffi MB, Bertollo LAC, Tanomtong A, Molina WF. Karyotypic changes and diversification time in Epinephelidae groupers (Perciformes). Implications on reproductive isolation. AN ACAD BRAS CIENC 2024; 96:e20221011. [PMID: 38597487 DOI: 10.1590/0001-3765202420221011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 06/26/2023] [Indexed: 04/11/2024] Open
Abstract
Groupers (Epinephelidae and Serranidae) have attracted special attention to fish farming, and their species offer good opportunities for successful hybridizations. Cytogenetic data allow a better understanding of the role of karyotypic diversification in the acquisition of post-zygotic reproductive isolation (RI). Thus, chromosomal analyses were performed on E. striatus (Caribbean Sea), E. coioides and E. tauvina (Indo-Pacific Region), using standard procedures and mapping of six repetitive DNA classes by the in situ hybridization. The three species have 2n=48 chromosomes. The karyotypes of E. coioides and E. striatus are composed only of acrocentric chromosomes (FN=48), while E. tauvina has 8 submetacentric chromosomes (FN=56). Heterochromatin has a preferential centromeric distribution, and the microsatellite repeats are dispersed throughout the chromosomes of all species. The 18S and 5S rDNA sites are unique but show a colocalization arrangement in E. tauvina and E. striatus. The chromosomal organization suggests that the three species still maintain a significant amount of syntenic regions. The range of the karyotype divergence and the RI levels showed low, but goes turn proportionally greater in relation to the divergence time between the parental species. The slow acquisition of postzygotic RI is consistent with the high karyotype homogeneity presented by Epinephelidae family.
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Affiliation(s)
- Karlla Danielle J Amorim
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Biologia Celular e Genética, Av. Senador Salgado Filho, s/n, Campus Universitário, Lagoa Nova, 59078-970 Natal, RN, Brazil
| | - Gideão W W F Costa
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Biologia Celular e Genética, Av. Senador Salgado Filho, s/n, Campus Universitário, Lagoa Nova, 59078-970 Natal, RN, Brazil
| | - Clóvis C Motta-Neto
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Biologia Celular e Genética, Av. Senador Salgado Filho, s/n, Campus Universitário, Lagoa Nova, 59078-970 Natal, RN, Brazil
| | - Rodrigo X Soares
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Biologia Celular e Genética, Av. Senador Salgado Filho, s/n, Campus Universitário, Lagoa Nova, 59078-970 Natal, RN, Brazil
| | - Amanda T Borges
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Biologia Celular e Genética, Av. Senador Salgado Filho, s/n, Campus Universitário, Lagoa Nova, 59078-970 Natal, RN, Brazil
| | - Daniel D Benetti
- University of Miami, Rosenstiel School of Marine and Atmospheric Science (RSMAS), 4600 Rickenbacker Causeway, Miami, FL 33149, USA
| | - Marcelo B Cioffi
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Citogenética de Peixes, Caixa Postal 676, 13565-905 São Carlos, SP, Brazil
| | - Luiz A C Bertollo
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Citogenética de Peixes, Caixa Postal 676, 13565-905 São Carlos, SP, Brazil
| | - Alongklod Tanomtong
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen, 40002,Thailand
- Toxic Substances in Livestock and Aquatic Animals Research Group, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Wagner F Molina
- Universidade Federal do Rio Grande do Norte, Centro de Biociências, Departamento de Biologia Celular e Genética, Av. Senador Salgado Filho, s/n, Campus Universitário, Lagoa Nova, 59078-970 Natal, RN, Brazil
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Mousavi SE, Grützner F, Patil JG. Enhanced mitotic arrest and chromosome resolution for cytogenetic analysis in the eastern mosquitofish, Gambusia holbrooki. Acta Histochem 2023; 125:152029. [PMID: 37062122 DOI: 10.1016/j.acthis.2023.152029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/18/2023]
Abstract
Maximising the number of cells arrested at metaphase and their resolution is fundamentally important for molecular cytogenetic investigations, particularly in fish, which typically yield low mitotic index and have highly condensed chromosomes. To overcome these limitations, fish were injected with a mitotic stimulator (the yeast, Saccharomyces cerevisiae) to improve the mitotic index, and the intercalating agent ethidium bromide to produce elongated chromosomes. Specifically, adults were injected with activated yeast and then Colcemid (0.025 µg/µl solution, 10 µl per 1 g of body weight) at 24-96 h post yeast injections, followed by chromosome preparations from multiple tissues. Results showed that gill tissue had the highest number of dividing cells at 72 h post yeast exposure with no significant (p > 0.05) differences between the sexes. Nonetheless, sex-specific differences in the mitotic index were observed in spleen, kidney, and liver, which may be attributed to sex-specific differences in immune responses. For elongation of mitotic chromosomes, individuals (both sexes) were first injected with activated yeast and after 48 h with ethidium bromide (2 or 4 µg/ml) and Colcemid (0.05 µg/µl solution, 10 µl per 1 g of body weight). Following which, animals were sampled at three time points (1, 4 and 8 h) for chromosome preparations. The results show that the optimum elongation of metaphase chromosomes of males and females was achieved by using 2 µg/ml and 4 µg/ml, respectively, for 1 h. Interestingly, the average mitotic chromosome length (μm) of males and females post-ethidium bromide exposure was significantly different (p < 0.05) for both concentrations, except at 1 h exposure for 2 µg/ml EtBr. Such differences can be attributed to overall chromosomal condensation differences between sexes. Regardless, the increased mitotic index and chromosome resolution could benefit cytogenetic studies in other fish species.
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Affiliation(s)
- Seyed Ehsan Mousavi
- Laboratory of Molecular Biology, Institute for Marine and Antarctic Studies, University of Tasmania, Taroona, TAS 7053, Australia; School of Medicine, University of Tasmania, Hobart, TAS 7000, Australia.
| | - Frank Grützner
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Jawahar G Patil
- Laboratory of Molecular Biology, Institute for Marine and Antarctic Studies, University of Tasmania, Taroona, TAS 7053, Australia
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Amorim KDJ, da Costa GWWF, Cioffi MDB, Tanomtong A, Bertollo LAC, Molina WF. A new view on the scenario of karyotypic stasis in Epinephelidae fish: Cytogenetic, historical, and biogeographic approaches. Genet Mol Biol 2021; 44:e20210122. [PMID: 34807969 PMCID: PMC8608104 DOI: 10.1590/1678-4685-gmb-2021-0122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/15/2021] [Indexed: 11/21/2022] Open
Abstract
Epinephelidae (groupers) is an astonishingly diverse group of carnivorous fish widely distributed in reef environments around the world, with growing economic importance. The first chromosomal inferences suggested a conservative scenario for the family. However, to date, this has not been validated using biogeographic and phylogenetic approaches. Thus, to estimate karyotype diversification among groupers, eight species from the Atlantic and Indian oceans were investigated using conventional cytogenetic protocols and fluorescence in situ hybridization of repetitive sequences (rDNA, microsatellites, transposable elements). Despite the remarkable persistence of some symplesiomorphic karyotype patterns, such as all species sharing 2n=48 and most preserve a basal karyotype (2n=48 acrocentrics), the chromosomal diversification in the family revealed an unsuspected evolutionary dynamic, where about 40% of the species escape from the ancestral karyotype pattern. These karyotype changes showed a relation with the historical biogeography, likely as a byproduct of the progressive occupancy of new areas (huge diversity of adaptive and speciation conditions). In this context, oceanic regions harboring more recent clades such as those of the Indo-Pacific, exhibited a higher karyotype diversity. Therefore, the karyotype evolution of Epinephelidae fits well with the expansion and geographic contingencies of its clades, providing a more complex and diverse scenario than previously assumed.
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Affiliation(s)
- Karlla Danielle Jorge Amorim
- Universidade Federal do Rio Grande do Norte, Departamento de Biologia Celular e Genética, Centro de Biociências, Natal, RN, Brazil
| | | | - Marcelo de Bello Cioffi
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Citogenética de Peixes, São Carlos, SP, Brazil
| | - Alongklod Tanomtong
- Khon Kaen University, Department of Biology, Faculty of Science, Muang, Khon Kaen, Thailand
- Khon Kaen University, Toxic Substances in Livestock and Aquatic Animals Research Group, Muang, Khon Kaen 40002, Thailand
| | - Luiz Antônio Carlos Bertollo
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, Laboratório de Citogenética de Peixes, São Carlos, SP, Brazil
| | - Wagner Franco Molina
- Universidade Federal do Rio Grande do Norte, Departamento de Biologia Celular e Genética, Centro de Biociências, Natal, RN, Brazil
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Xue L, Gao Y, Wu M, Tian T, Fan H, Huang Y, Huang Z, Li D, Xu L. Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair. Genome Biol 2021; 22:203. [PMID: 34253240 PMCID: PMC8273981 DOI: 10.1186/s13059-021-02430-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/01/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The origin of sex chromosomes requires the establishment of recombination suppression between the proto-sex chromosomes. In many fish species, the sex chromosome pair is homomorphic with a recent origin, providing species for studying how and why recombination suppression evolved in the initial stages of sex chromosome differentiation, but this requires accurate sequence assembly of the X and Y (or Z and W) chromosomes, which may be difficult if they are recently diverged. RESULTS Here we produce a haplotype-resolved genome assembly of zig-zag eel (Mastacembelus armatus), an aquaculture fish, at the chromosomal scale. The diploid assembly is nearly gap-free, and in most chromosomes, we resolve the centromeric and subtelomeric heterochromatic sequences. In particular, the Y chromosome, including its highly repetitive short arm, has zero gaps. Using resequencing data, we identify a ~7 Mb fully sex-linked region (SLR), spanning the sex chromosome centromere and almost entirely embedded in the pericentromeric heterochromatin. The SLRs on the X and Y chromosomes are almost identical in sequence and gene content, but both are repetitive and heterochromatic, consistent with zero or low recombination. We further identify an HMG-domain containing gene HMGN6 in the SLR as a candidate sex-determining gene that is expressed at the onset of testis development. CONCLUSIONS Our study supports the idea that preexisting regions of low recombination, such as pericentromeric regions, can give rise to SLR in the absence of structural variations between the proto-sex chromosomes.
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Affiliation(s)
- Lingzhan Xue
- College of Fisheries, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, 430070, China.,Aquaculture and Genetic Breeding Laboratory, Freshwater Fisheries Research Institute of Fujian, Fuzhou, 350002, China
| | - Yu Gao
- College of Animal Science and Technology, Key Laboratory for Plateau Fishery Resources Conservation and Sustainable Utilization of Yunnan Province, Yunnan Agricultural University, Kunming, 650201, China
| | - Meiying Wu
- Aquaculture and Genetic Breeding Laboratory, Freshwater Fisheries Research Institute of Fujian, Fuzhou, 350002, China
| | - Tian Tian
- Aquaculture and Genetic Breeding Laboratory, Freshwater Fisheries Research Institute of Fujian, Fuzhou, 350002, China
| | - Haiping Fan
- Freshwater Fisheries Research Institute of Fujian, Fuzhou, 350002, China
| | - Yongji Huang
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Zhen Huang
- Fujian Key Laboratory of Developmental and Neural Biology & Southern Center for Biomedical Research, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China. .,Fujian Key Laboratory of Special Marine Bio-resources Sustainable Utilization, Fuzhou, 350117, Fujian, China.
| | - Dapeng Li
- College of Fisheries, Hubei Provincial Engineering Laboratory for Pond Aquaculture, Huazhong Agricultural University, Wuhan, 430070, China. .,Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, 430070, China.
| | - Luohao Xu
- Department of Neurosciences and Developmental Biology, University of Vienna, 1090, Vienna, Austria.
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Soares LB, Paim FG, Ramos LP, Foresti F, Oliveira C. Molecular cytogenetic analysis and the establishment of a cell culture in the fish species Hollandichthys multifasciatus (Eigenmann & Norris, 1900) (Characiformes, Characidae). Genet Mol Biol 2021; 44:e20200260. [PMID: 33877256 PMCID: PMC8056886 DOI: 10.1590/1678-4685-gmb-2020-0260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 02/07/2021] [Indexed: 11/22/2022] Open
Abstract
Hollandichthys is a fish genus of the family Characidae that
was until recently considered to be monotypic, with cytogenetic, morphological,
and molecular data being restricted to a few local populations. In the present
study, the karyotype of a population of Hollandichthys
multifasciatus was analyzed using classical and molecular
cytogenetic approaches for the investigation of potential markers that could
provide new perspectives on the cytotaxonomy. H. multifasciatus
presented a diploid number of 2n=50 chromosomes and a karyotype formula of
8m+10sm+32st. A single pair of chromosomes presented Ag-NORs signals, which
coincided with the 18S rDNA sites visualized by FISH, whilst the 5S rDNA
sequences were mapped in two chromosome pairs. The distribution of the U snRNA
genes was mapped on the Hollandichthys chromosomes for the
first time, with the probes revealing the presence of the U1 snDNA on the
chromosomes of pair 20, U2 on pairs 6 and 19, U4 on pair 16, and U6 on the
chromosomes of pair 11. The results of the present study indicated karyotypic
differences in comparison with the other populations of H.
multifasciatus studied previously, reinforcing the need for further
research to identify isolated populations or the potential existence of cryptic
Hollandichthys species.
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Affiliation(s)
- Letícia Batista Soares
- Universidade Estadual Paulista "Júlio de Mesquita Filho", Instituto de Biociências, Laboratório de Biologia e Genética de Peixes, Botucatu, SP, Brazil
| | - Fabilene Gomes Paim
- Universidade Estadual Paulista "Júlio de Mesquita Filho", Instituto de Biociências, Laboratório de Biologia e Genética de Peixes, Botucatu, SP, Brazil
| | - Lucas Peres Ramos
- Universidade Estadual Paulista "Júlio de Mesquita Filho", Instituto de Biociências, Laboratório de Biologia e Genética de Peixes, Botucatu, SP, Brazil
| | - Fausto Foresti
- Universidade Estadual Paulista "Júlio de Mesquita Filho", Instituto de Biociências, Laboratório de Biologia e Genética de Peixes, Botucatu, SP, Brazil
| | - Claudio Oliveira
- Universidade Estadual Paulista "Júlio de Mesquita Filho", Instituto de Biociências, Laboratório de Biologia e Genética de Peixes, Botucatu, SP, Brazil
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Ghigliotti L, Christiansen JS, Carlig E, Di Blasi D, Pisano E. Latitudinal Cline in Chromosome Numbers of Ice Cod A. glacialis (Gadidae) from Northeast Greenland. Genes (Basel) 2020; 11:E1515. [PMID: 33352937 DOI: 10.3390/genes11121515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 11/17/2022] Open
Abstract
The ice cod Arctogadus glacialis (Peters, 1872) is one of the few fish species endemic to the Arctic. With a circumpolar distribution, the species is confined to the fjords and shelves of the Arctic seas. Biological information on A. glacialis is scarce, with genomic information restricted to microsatellites. Within the frame of the TUNU-Programme: Arctic Ocean Fishes-Diversity, Adaptation and Conservation, we studied A. glacialis at the chromosomal level to explore fish diversity and evolutionary aspects. The analysis of over 50 individuals from the Northeast Greenland fjords between latitudes 71°09' N and 76°42' N revealed a remarkable intraspecific diversity epitomized by chromosome numbers spanning from 28 to 33, the occurrence of putative B chromosomes, and diversified patterns of distribution of heterochromatin and rDNAs. The number of B chromosomes followed a latitudinal gradient from 0-2 in the north to 2-5 in the south. Considering the benthic and rather stationary life history of this species, the observed chromosomal differences might have arisen independently, possibly driven and/or fostered by the dynamics of repetitive sequences, and are being fixed in relatively isolated fjord populations. The resulting latitudinal cline we observe today might have repercussions on the fate of local populations facing the ongoing climate-driven environmental changes.
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Araya-Jaime C, Palma-Rojas C, Brand EV, Silva A. Cytogenetic characterization, rDNA mapping and quantification of the nuclear DNA content in Seriolella violacea Guichenot, 1848 (Perciformes, Centrolophidae). Comp Cytogenet 2020; 14:319-328. [PMID: 32754305 PMCID: PMC7381430 DOI: 10.3897/compcytogen.v14i3.53087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/05/2020] [Indexed: 05/27/2023]
Abstract
Seriolella violacea Guichenot, 1848 is an important component of the fish fauna of the Chilean coast and is of great economic interest. Cytogenetic information for the family Centrolophidae is lacking and the genomic size of five of the twenty-eight species described for this family are is barely known. This study aimed to describe for the first time the karyotype structure via classical and molecular cytogenetics analysis with the goal of identifying the constitutive heterochromatin distribution, chromosome organization of rDNA sequences and quantification of nuclear DNA content. The karyotype of S. violacea is composed of 48 chromosomes, with the presence of conspicuous blocks of heterochromatin on chromosomal pairs one and two. FISH assay with a 5S rDNA probe, revealed the presence of fluorescent markings on the heterochromatic block of pair one. The 18S rDNA sites are located exclusively on pair two, characterizing this pair as the carrier of the NOR. Finally, the genomic size of S. violacea was estimated at 0.59 pg of DNA as C-value. This work represents the first effort to document the karyotype structure and physical organization of the rDNA sequences in the Seriolella genome, contributing with new information to improve our understanding of chromosomal evolution and genomic organization in marine perciforms.
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Affiliation(s)
- Cristian Araya-Jaime
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, Casilla 554, La Serena, ChileUniversidad de La SerenaLa SerenaChile
- Laboratorio de Genética y Citogenética Vegetal, Departamento de Biología, Universidad de La Serena. La Serena, ChileUniversidad Católica del Norte Sede CoquimboCoquimboChile
| | - Claudio Palma-Rojas
- Laboratorio de Genética y Citogenética Vegetal, Departamento de Biología, Universidad de La Serena. La Serena, ChileUniversidad Católica del Norte Sede CoquimboCoquimboChile
| | - Elisabeth Von Brand
- Departamento de Biología Marina Facultad de Ciencias del Mar, Universidad Católica del Norte Sede Coquimbo, Casilla 117, Coquimbo, ChileUniversidad de La SerenaLa SerenaChile
| | - Alfonso Silva
- Laboratorio Cultivo de Peces, Facultad de Ciencias del Mar, Universidad Católica del Norte Sede Coquimbo, Casilla 117, Coquimbo, ChileUniversidad Católica del Norte Sede CoquimboCoquimboChile
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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