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dos Santos AG, Souza JFDSE, Soares SC, Nakayama CM, Feldberg E. Chromosomal characterization of three species of Serrasalmini (Serrasalmidae: Characiformes). Genet Mol Biol 2023; 46:e20230088. [PMID: 37992304 PMCID: PMC10664975 DOI: 10.1590/1678-4685-gmb-2023-0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 10/10/2023] [Indexed: 11/24/2023] Open
Abstract
The tribe Serrasalmini is a diverse group with paraphyletic genera and taxonomic uncertainties. Several studies have been carried out in this group of fish in order to understand this problem, including the cytogenetic approach. In this study, three species of a clade of Serrasalmini were characterized cytogenetically - Pristobrycon striolatus, Catoprion absconditus and Pygopristis denticulatus. The three species presented diploid number (2n) equal to 62 chromosomes, of one and two arms, with karyotypic formulas and species-specific fundamental numbers. Heterochromatin is centromeric and terminal (bi-telomeric) in most chromosomes, with a conspicuous interstitial block at pair 1 (m) in all three species. The nucleolar organizer regions were multiple and C-band positive, and their location was confirmed via 18S ribosomal DNA mapping; however, with additional sites. The 5S rDNA was located in interstitial region of long arm of pair 1 (m), in the three species (homeologous). Moreover, we observed synteny between 18S and 5S in the species C. absconditus and P. denticulatus, which, according to fiber-FISH, are interspersed. Thus, the maintenance of 2n (62) evidences the diversification of chromosomal formulas within the clade by non-Robertsonian rearrangements and reflects the paraphyly of the related species.
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Affiliation(s)
- Alan Gomes dos Santos
- Instituto Nacional de Pesquisas da Amazônia (INPA), Programa de
Pós-graduação em Genética, Conservação e Biologia Evolutiva, Laboratório de Genética
Animal, Manaus, AM, Brazil
| | - José Francisco de Sousa e Souza
- Instituto Nacional de Pesquisas da Amazônia (INPA), Programa de
Pós-graduação em Genética, Conservação e Biologia Evolutiva, Laboratório de Genética
Animal, Manaus, AM, Brazil
| | - Simone Cardoso Soares
- Instituto Nacional de Pesquisas da Amazônia (INPA), Programa de
Pós-graduação em Genética, Conservação e Biologia Evolutiva, Laboratório de Genética
Animal, Manaus, AM, Brazil
| | - Celeste Mutuko Nakayama
- Instituto Nacional de Pesquisas da Amazônia (INPA), Coordenação de
Biodiversidade, Laboratório de Genética Animal, Manaus, AM, Brazil
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia (INPA), Programa de
Pós-graduação em Genética, Conservação e Biologia Evolutiva, Laboratório de Genética
Animal, Manaus, AM, Brazil
- Instituto Nacional de Pesquisas da Amazônia (INPA), Coordenação de
Biodiversidade, Laboratório de Genética Animal, Manaus, AM, Brazil
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Telomeres and Their Neighbors. Genes (Basel) 2022; 13:genes13091663. [PMID: 36140830 PMCID: PMC9498494 DOI: 10.3390/genes13091663] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Telomeres are essential structures formed from satellite DNA repeats at the ends of chromosomes in most eukaryotes. Satellite DNA repeat sequences are useful markers for karyotyping, but have a more enigmatic role in the eukaryotic cell. Much work has been done to investigate the structure and arrangement of repetitive DNA elements in classical models with implications for species evolution. Still more is needed until there is a complete picture of the biological function of DNA satellite sequences, particularly when considering non-model organisms. Celebrating Gregor Mendel’s anniversary by going to the roots, this review is designed to inspire and aid new research into telomeres and satellites with a particular focus on non-model organisms and accessible experimental and in silico methods that do not require specialized equipment or expensive materials. We describe how to identify telomere (and satellite) repeats giving many examples of published (and some unpublished) data from these techniques to illustrate the principles behind the experiments. We also present advice on how to perform and analyse such experiments, including details of common pitfalls. Our examples are a selection of recent developments and underexplored areas of research from the past. As a nod to Mendel’s early work, we use many examples from plants and insects, especially as much recent work has expanded beyond the human and yeast models traditional in telomere research. We give a general introduction to the accepted knowledge of telomere and satellite systems and include references to specialized reviews for the interested reader.
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Multiple heterochromatin diversification events in the genome of fungus-farming ants: insights from repetitive sequences. Chromosoma 2022; 131:59-75. [PMID: 35325297 DOI: 10.1007/s00412-022-00770-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/18/2022] [Accepted: 02/21/2022] [Indexed: 11/03/2022]
Abstract
A substantial portion of the eukaryotic genome includes repetitive DNA, which is important for its stability, regulation, and architecture. Fungus-farming ant genomes show remarkable structural rearrangement rates that were necessary for the establishment of their agriculture-based lifestyle, highlighting the relevance of this peculiar group in understanding the repetitive portion of ant genome. Chromosomal banding studies are in accordance with genomic data because they show that repetitive heterochromatic sequences of basal and derivative Attina species are GC-rich, an uncommon trait in Formicidae. To understand the evolutionary dynamics of heterochromatin in Attina, we compared GC-rich heterochromatin patterns between the Paleoattina and Neoattina clades of this subtribe. To this end, we hybridized the Mrel-C0t probe (highly and moderately repetitive DNA) obtained from Mycetomoellerius relictus, Neoattina with GC-rich heterochromatin, in karyotypes of Paleoattina and Neoattina species. Additionally, we mapped the repetitive sequences (GA)15 and (TTAGG)6 in species of the two clades to investigate their organization and evolutionary patterns in the genome of Attina. The Mrel-C0t probe marked the heterochromatin in M. relictus, in other Mycetomoellerius spp., and in species of Mycetarotes, Cyphomyrmex, and Sericomyrmex (Neoattina). In Mycetomoellerius urichii, only pericentromeric heterochromatin was marked with Mrel-C0t. No marking was observed in Paleoattina species or in Atta and Acromyrmex (Neoattina). These results indicated that different evolutionary events led to heterochromatin differentiation in Attina. The most likely hypothesis is that GC-rich heterochromatin arose in the common ancestor of the two clades and accumulated various changes throughout evolution. The sequences (GA)15 and (TTAGG)6 located in euchromatin and telomeres, respectively, showed more homogeneous results among the species.
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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] [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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Zhao C, Zhang Y, Qin H, Wang C, Huang X, Yang L, Yu T, Xu X, Luo X, Qin Q, Liu S. Organization and expression analysis of 5S and 45S ribosomal DNA clusters in autotetraploid Carassius auratus. BMC Ecol Evol 2021; 21:201. [PMID: 34740327 PMCID: PMC8569995 DOI: 10.1186/s12862-021-01918-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 09/24/2021] [Indexed: 12/03/2022] Open
Abstract
Background Autotetraploid Carassius auratus (4n = 200, RRRR) (abbreviated as 4nRR) is derived from whole genome duplication of Carassius auratus red var. (2n = 100, RR) (abbreviated as RCC). Ribosome DNA (rDNA) is often used to study molecular evolution of repeated sequences because it has high copy number and special conserved coding regions in genomes. In this study, we analysed the sequences (5S, ITS1-5.8S-ITS2 region), structure, methylation level (NTS and IGS), and expression level (5S and 18S) of 5S and 45S ribosomal RNA (rRNA) genes in 4nRR and RCC in order to elucidate the effects of autotetraploidization on rDNA in fish. Results Results showed that there was high sequence similarity of 5S, 5.8S and ITS1 region between 4nRR and RCC. This study also identified two different types of ITS2 region in 4nRR and predicted the secondary structure of ITS2. It turns out that both secondary structures are functional. Compared with RCC, there was no significant difference in NTS (5S rRNA) methylation level, but the expression level of 5S rRNA was lower in 4nRR, indicating that methylation had little effect on the expression level in 4nRR. IGS (45S rRNA) was hypermethylated in 4nRR compared to RCC, but the expression of 18S rRNA gene was no significantly different from that in RCC, indicating that methylation regulation affected gene expression in 4nRR. Conclusion The above studies initially revealed the effects of autotetraploidization on the structure and function of 5S and 45S rRNA in Carassius auratus, and provided a theoretical support for the systematic study of the evolution pattern and characteristics of rDNA in vertebrates.
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Affiliation(s)
- Chun Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Yuxin Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Huan Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chongqing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Xu Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Li Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Tingting Yu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Xidan Xu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Xiang Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
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Pinheiro Figliuolo VS, Ferreira AMV, Guimarães EMC, de Sousa E Souza JF, Feldberg E, Gross MC. Cryptic Diversity in the Terminal Portion of the Chromosomes of the Dogtooth Characins, Family Cynodontidae (Ostariophysi: Characiformes). Zebrafish 2021; 18:221-230. [PMID: 33847525 DOI: 10.1089/zeb.2020.1973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The chromosomes of the dogtooth characins, fish species of the family Cynodontidae, have only a relatively small amount of heterochromatin, including the terminal portion. Curiously, in the cynodontid Cynodon gibbus, the terminal portion is rich in repetitive DNAs, including transposable retroelements and microsatellite sequences. Given this, this study investigated the composition of the terminal portion of the chromosomes of two cynodontid species (Rhaphiodon vulpinus and Hydrolycus armatus), to compile a database for the evaluation of all three cynodontid genera, and in particular, verify the possible tendency for the accumulation of repetitive DNAs in the terminal portion of the chromosomes of C. gibbus, H. armatus, and R. vulpinus. The Rex1, Rex3, and Rex6 transposable retroelements and the (CA)15, (GA)15, (GATA)8, (GACA)8, (CAT)10, and (CAC)10 microsatellite motifs are found primarily in the terminal portion of the chromosomes of the species analyzed in this study, except R. vulpinus, which has no evidence of the presence of Rex1 or Rex3 through the fluorescent in situ hybridization technique. The mapping of the repetitive sequences, principally the microsatellite motifs, indicates a marked tendency for the accumulation of these sequences in the terminal portions of the chromosomes, which may have played a fundamental role in the differentiation of the three species.
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Affiliation(s)
| | | | | | | | - Eliana Feldberg
- Laboratory of Animal Genetics, National Institute of Amazonian Research (INPA), Manaus, Brazil
| | - Maria Claudia Gross
- Institute for Natural and Life Sciences, Federal University of Latin American Integration, Foz do Iguaçu, Brazil
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Sevilleno SS, Ju YH, Kim JS, Mancia FH, Byeon EJ, Cabahug RA, Hwang YJ. Cytogenetic analysis of Bienertia sinuspersici Akhani as the first step in genome sequencing. Genes Genomics 2020; 42:337-345. [PMID: 31902107 DOI: 10.1007/s13258-019-00908-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/18/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND C4 plants are efficient in suppressing photorespiration and enhancing carbon gain as compared to C3 plants. Bienertia sinuspersici Akhani is one of the few species in the family Amaranthaceae that can perform C4 photosynthesis within individual chlorenchyma cells, without the conventional Kranz anatomy in its leaf. This plant is salt-tolerant and is well-adapted to thrive in hot and humid climates. To date, there have been no reported cytogenetic analyses yet on this species. OBJECTIVE This study aims to provide a cytogenetic analysis of B. sinuspersici as the first step in genome sequencing. METHODS Fluorescence in situ hybridization (FISH) karyotype analysis was conducted using the metaphase chromosomes of B. sinuspersici probed with 5S and 45S rDNA and Arabidopsis-type telomeric repeats. RESULTS Results of the cytogenetic analysis confirmed that B. sinuspersici has 2n = 2x = 18 consisting of nine pairs of metacentric chromosomes. Two loci of 45S rDNA were found on the distal regions of the short arm of chromosome 7. Nine loci of 5S rDNA were found in the pericentromeric regions of chromosomes 1, 3, 4, 6, and 8, which also colocalized with Arabidopsis-type telomeric repeats; while four loci in the interstitial regions of chromosome 5 and 8 can be observed. The single locus of 5S rDNA that was found in chromosome 8 appears to be hemizygous. CONCLUSION The FISH karyotype analysis, based on the combination of rDNAs, telomeric tandem repeat markers and C0t DNA chromosome landmarks, allowed efficient chromosome identification and provided useful information in characterizing the genome of B. sinuspersici.
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Affiliation(s)
| | - Yoon Ha Ju
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jung Sun Kim
- Genetics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Franklin Hinosa Mancia
- Department of Environmental Horticulture, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Eun Ju Byeon
- Genetics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Raisa Aone Cabahug
- Chromosome Research Institute, Sahmyook University, Seoul, 01795, Republic of Korea
| | - Yoon-Jung Hwang
- Department of Convergence Science, Sahmyook University, Seoul, 01795, Republic of Korea.
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Araújo da Silva F, Feldberg E, Moura Carvalho ND, Hernández Rangel SM, Schneider CH, Carvalho-Zilse GA, Fonsêca da Silva V, Gross MC. Effects of environmental pollution on the rDNAomics of Amazonian fish. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 252:180-187. [PMID: 31146233 DOI: 10.1016/j.envpol.2019.05.112] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 06/09/2023]
Abstract
Pollution is a growing environmental problem throughout the world, and the impact of human activities on biodiversity and the genetic variability of natural populations is increasingly preoccupying, given that adaptive processes depend on this variability, in particular that found in the repetitive DNA. In the present study, the mitochondrial DNA (COI) and the distribution of repetitive DNA sequences (18S and 5S rDNA) in the fish genome were analysed in fish populations inhabiting both polluted and unpolluted waters in the northern Amazon basin. The results indicate highly complex ribosomal sequences in the fish genome from the polluted environment because these sequences are involved primarily in the maintenance of genome integrity, mediated by a systematic increase in the number of copies of the ribosomal DNA in response to changes in environmental conditions.
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Affiliation(s)
- Francijara Araújo da Silva
- Programa de Pós-Graduação Em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil.
| | - Eliana Feldberg
- Programa de Pós-Graduação Em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Natália Dayane Moura Carvalho
- Escola Superior de Ciências da Saúde, Programa de Pós-Graduação Em Biotecnologia e Recursos Naturais da Amazônia, Universidade do Estado do Amazonas, Manaus, AM, Brazil
| | | | | | - Gislene Almeida Carvalho-Zilse
- Programa de Pós-Graduação Em Genética, Conservação e Biologia Evolutiva, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | | | - Maria Claudia Gross
- Instituto de Ciências da Vida e da Natureza, Universidade Federal de Integração Latino Americana, Foz do Iguaçu, PR, Brazil
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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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Ferreira M, Garcia C, Matoso DA, de Jesus IS, Feldberg E. A new multiple sex chromosome system X1X1X2X2/X1Y1X2Y2 in Siluriformes: cytogenetic characterization of Bunocephalus coracoideus (Aspredinidae). Genetica 2016; 144:591-599. [DOI: 10.1007/s10709-016-9927-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 09/19/2016] [Indexed: 11/29/2022]
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Carvalho NDM, Carmo E, Neves RO, Schneider CH, Gross MC. Differential repetitive DNA composition in the centromeric region of chromosomes of Amazonian lizard species in the family Teiidae. COMPARATIVE CYTOGENETICS 2016; 10:203-217. [PMID: 27551343 PMCID: PMC4977797 DOI: 10.3897/compcytogen.v10i2.7081] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 02/18/2016] [Indexed: 06/06/2023]
Abstract
Differences in heterochromatin distribution patterns and its composition were observed in Amazonian teiid species. Studies have shown repetitive DNA harbors heterochromatic blocks which are located in centromeric and telomeric regions in Ameiva ameiva (Linnaeus, 1758), Kentropyx calcarata (Spix, 1825), Kentropyx pelviceps (Cope, 1868), and Tupinambis teguixin (Linnaeus, 1758). In Cnemidophorus sp.1, repetitive DNA has multiple signals along all chromosomes. The aim of this study was to characterize moderately and highly repetitive DNA sequences by C ot1-DNA from Ameiva ameiva and Cnemidophorus sp.1 genomes through cloning and DNA sequencing, as well as mapping them chromosomally to better understand its organization and genome dynamics. The results of sequencing of DNA libraries obtained by C ot1-DNA showed that different microsatellites, transposons, retrotransposons, and some gene families also comprise the fraction of repetitive DNA in the teiid species. FISH using C ot1-DNA probes isolated from both Ameiva ameiva and Cnemidophorus sp.1 showed these sequences mainly located in heterochromatic centromeric, and telomeric regions in Ameiva ameiva, Kentropyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin chromosomes, indicating they play structural and functional roles in the genome of these species. In Cnemidophorus sp.1, C ot1-DNA probe isolated from Ameiva ameiva had multiple interstitial signals on chromosomes, whereas mapping of C ot1-DNA isolated from the Ameiva ameiva and Cnemidophorus sp.1 highlighted centromeric regions of some chromosomes. Thus, the data obtained showed that many repetitive DNA classes are part of the genome of Ameiva ameiva, Cnemidophorus sp.1, Kentroyx calcarata, Kentropyx pelviceps, and Tupinambis teguixin, and these sequences are shared among the analyzed teiid species, but they were not always allocated at the same chromosome position.
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Affiliation(s)
- Natalia D. M. Carvalho
- Laboratório de Citogenômica Animal, Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Estrada do Contorno 3000, Aleixo, CEP 69077-000 - Manaus, AM – Brazil
| | - Edson Carmo
- Laboratório de Tecnologia de DNA, Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Estrada do Contorno 3000, Aleixo, CEP 69077-000 - Manaus, AM – Brazil
| | - Rogerio O. Neves
- Laboratório de Tecnologia de DNA, Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Estrada do Contorno 3000, Aleixo, CEP 69077-000 - Manaus, AM – Brazil
| | - Carlos Henrique Schneider
- Laboratório de Citogenômica Animal, Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Estrada do Contorno 3000, Aleixo, CEP 69077-000 - Manaus, AM – Brazil
| | - Maria Claudia Gross
- Laboratório de Citogenômica Animal, Universidade Federal do Amazonas, Instituto de Ciências Biológicas, Estrada do Contorno 3000, Aleixo, CEP 69077-000 - Manaus, AM – Brazil
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