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Khensuwan S, Sassi FDMC, Moraes RLR, Jantarat S, Seetapan K, Phintong K, Thongnetr W, Kaewsri S, Jumrusthanasan S, Supiwong W, Rab P, Tanomtong A, Liehr T, Cioffi MB. Chromosomes of Asian Cyprinid Fishes: Genomic Differences in Conserved Karyotypes of 'Poropuntiinae' (Teleostei, Cyprinidae). Animals (Basel) 2023; 13:ani13081415. [PMID: 37106978 PMCID: PMC10135121 DOI: 10.3390/ani13081415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/13/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
The representatives of cyprinid lineage 'Poropuntiinae' with 16 recognized genera and around 100 species form a significant part of Southeast Asian ichthyofauna. Cytogenetics are valuable when studying fish evolution, especially the dynamics of repetitive DNAs, such as ribosomal DNAs (5S and 18S) and microsatellites, that can vary between species. Here, karyotypes of seven 'poropuntiin' species, namely Cosmochilus harmandi, Cyclocheilichthys apogon, Hypsibarbus malcomi, H. wetmorei, Mystacoleucus chilopterus, M. ectypus, and Puntioplties proctozysron occurring in Thailand were examined using conventional and molecular cytogenetic protocols. Variable numbers of uni- and bi-armed chromosomes indicated widespread chromosome rearrangements with a stable diploid chromosome number (2n) of 50. Examination with fluorescence in situ hybridization using major and minor ribosomal probes showed that Cosmochilus harmandi, Cyclocheilichthys apogon, and Puntioplites proctozystron all had one chromosomal pair with 5S rDNA sites. However, more than two sites were found in Hypsibarbus malcolmi, H. wetmorei, Mystacoleucus chilopterus, and M. ectypus. The number of chromosomes with 18S rDNA sites varied amongst their karyotypes from one to three; additionally, comparative genomic hybridization and microsatellite patterns varied among species. Our results reinforce the trend of chromosomal evolution in cyprinifom fishes, with major chromosomal rearrangements, while conserving their 2n.
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Affiliation(s)
- Sudarat Khensuwan
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Francisco de M C Sassi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, Brazil
| | - Renata L R Moraes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, Brazil
| | - Sitthisak Jantarat
- Department of Science, Faculty of Science and Technology, Prince of Songkla University, Pattani 94000, Thailand
| | - Kriengkrai Seetapan
- School of Agriculture and Natural Resources, University of Phayao, Tumbol Maeka, Muang, Phayao 56000, Thailand
| | - Krit Phintong
- Department of Fundamental Science, Faculty of Science and Technology, Surindra Rajabhat University, Muang, Surin 32000, Thailand
| | - Weera Thongnetr
- Division of Biology, Department of Science, Faculty of Science and Technology, Rajamangala University of Technology Krungthep, Bangkok 10120, Thailand
| | - Sarawut Kaewsri
- Program in Biology, Faculty of Science, Buriram Rajabhat University, Muang, Buriram 31000, Thailand
| | - Sarun Jumrusthanasan
- Program in Biology, Faculty of Science, Buriram Rajabhat University, Muang, Buriram 31000, Thailand
| | - Weerayuth Supiwong
- Faculty of Applied Science and Engineering, Khon Kaen University, Nong Khai Campus, Muang, Nong Khai 43000, Thailand
| | - Petr Rab
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277 21 Liběchov, Czech Republic
| | - Alongklod Tanomtong
- Department of Biology, Faculty of Science, Khon Kaen University, Muang, Khon Kaen 40002, Thailand
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, 07747 Jena, Germany
| | - Marcelo B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos 13565-905, Brazil
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2
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de Oliveira EA, Bertollo LAC, Rab P, Ezaz T, Yano CF, Hatanaka T, Jegede OI, Tanomtong A, Liehr T, Sember A, Maruyama SR, Feldberg E, Viana PF, Cioffi MDB. Cytogenetics, genomics and biodiversity of the South American and African Arapaimidae fish family (Teleostei, Osteoglossiformes). PLoS One 2019; 14:e0214225. [PMID: 30908514 PMCID: PMC6433368 DOI: 10.1371/journal.pone.0214225] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 03/09/2019] [Indexed: 11/19/2022] Open
Abstract
Osteoglossiformes represents one of the most ancestral teleost lineages, currently widespread over almost all continents, except for Antarctica. However, data involving advanced molecular cytogenetics or comparative genomics are yet largely limited for this fish group. Therefore, the present investigations focus on the osteoglossiform family Arapaimidae, studying a unique fish model group with advanced molecular cytogenetic genomic tools. The aim is to better explore and clarify certain events and factors that had impact on evolutionary history of this fish group. For that, both South American and African representatives of Arapaimidae, namely Arapaima gigas and Heterotis niloticus, were examined. Both species differed markedly by diploid chromosome numbers, with 2n = 56 found in A. gigas and 2n = 40 exhibited by H. niloticus. Conventional cytogenetics along with fluorescence in situ hybridization revealed some general trends shared by most osteoglossiform species analyzed thus far, such as the presence of only one chromosome pair bearing 18S and 5S rDNA sites and karyotypes dominated by acrocentric chromosomes, resembling thus the patterns of hypothetical ancestral teleost karyotype. Furthermore, the genomes of A. gigas and H. niloticus display remarkable divergence in terms of repetitive DNA content and distribution, as revealed by comparative genomic hybridization (CGH). On the other hand, genomic diversity of single copy sequences studied through principal component analyses (PCA) based on SNP alleles genotyped by the DArT seq procedure demonstrated a very low genetic distance between the South American and African Arapaimidae species; this pattern contrasts sharply with the scenario found in other osteoglossiform species. Underlying evolutionary mechanisms potentially explaining the obtained data have been suggested and discussed.
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Affiliation(s)
- Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
- Secretaria de Estado de Educação de Mato Grosso–SEDUC-MT, Cuiabá, MT, Brazil
| | - Luiz Antonio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
| | - Petr Rab
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Czech Republic
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, Australia
| | - Cassia Fernanda Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
| | | | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, KhonKaen University, Muang, KhonKaen, Thailand
| | - Thomas Liehr
- Institute of Human Genetics, University Hospital Jena, Jena, Germany
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Czech Republic
| | - Sandra Regina Maruyama
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
| | - Eliana Feldberg
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Laboratório de Genética Animal, Petrópolis, CEP: Manaus, AM, Brazil
| | - Patrik Ferreira Viana
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Laboratório de Genética Animal, Petrópolis, CEP: Manaus, AM, Brazil
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, SP, Brazil
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3
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Barby FF, Bertollo LAC, de Oliveira EA, Yano CF, Hatanaka T, Ráb P, Sember A, Ezaz T, Artoni RF, Liehr T, Al-Rikabi ABH, Trifonov V, de Oliveira EHC, Molina WF, Jegede OI, Tanomtong A, de Bello Cioffi M. Emerging patterns of genome organization in Notopteridae species (Teleostei, Osteoglossiformes) as revealed by Zoo-FISH and Comparative Genomic Hybridization (CGH). Sci Rep 2019; 9:1112. [PMID: 30718776 PMCID: PMC6361938 DOI: 10.1038/s41598-019-38617-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 01/03/2019] [Indexed: 11/09/2022] Open
Abstract
Notopteridae (Teleostei, Osteoglossiformes) represents an old fish lineage with ten currently recognized species distributed in African and Southeastern Asian rivers. Their karyotype structures and diploid numbers remained conserved over long evolutionary periods, since African and Asian lineages diverged approximately 120 Mya. However, a significant genetic diversity was already identified for these species using molecular data. Thus, why the evolutionary relationships within Notopteridae are so diverse at the genomic level but so conserved in terms of their karyotypes? In an attempt to develop a more comprehensive picture of the karyotype and genome evolution in Notopteridae, we performed comparative genomic hybridization (CGH) and cross-species (Zoo-FISH) whole chromosome painting experiments to explore chromosome-scale intergenomic divergence among seven notopterid species, collected in different African and Southeast Asian river basins. CGH demonstrated an advanced stage of sequence divergence among the species and Zoo-FISH experiments showed diffuse and limited homology on inter-generic level, showing a temporal reduction of evolutionarily conserved syntenic regions. The sharing of a conserved chromosomal region revealed by Zoo-FISH in these species provides perspectives that several other homologous syntenic regions have remained conserved among their genomes despite long temporal isolation. In summary, Notopteridae is an interesting model for tracking the chromosome evolution as it is (i) ancestral vertebrate group with Gondwanan distribution and (ii) an example of animal group exhibiting karyotype stasis. The present study brings new insights into degree of genome divergence vs. conservation at chromosomal and sub-chromosomal level in representative sampling of this group.
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Affiliation(s)
- Felipe Faix Barby
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil
| | - Luiz Antônio Carlos Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil
| | - Ezequiel Aguiar de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil
| | - Cassia Fernanda Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic
| | - Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, Liběchov, 277 21, Czech Republic
| | - Tariq Ezaz
- Institute for Applied Ecology, University of Canberra, Canberra, ACT 2617, Australia
| | - Roberto Ferreira Artoni
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | - Thomas Liehr
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | | | - Vladimir Trifonov
- Molecular and Cellular Biology, Russian Academy of Sciences, Novosibirsk, Russia
| | - Edivaldo H C de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Belém, Brazil
| | - Wagner Franco Molina
- Department of Cellular Biology and Genetics, Biosciences Center, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Oladele Ilesanmi Jegede
- Department of Fisheries and Aquaculture, Adamawa State University, P.M.B. 25, Mubi, Adamawa State, Nigeria
| | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, KhonKaen University, Muang, KhonKaen, 40002, Thailand
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz Km. 235, C.P. 676, São Carlos, SP, 13565-905, Brazil.
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Sember A, Bertollo LAC, Ráb P, Yano CF, Hatanaka T, de Oliveira EA, Cioffi MDB. Sex Chromosome Evolution and Genomic Divergence in the Fish Hoplias malabaricus (Characiformes, Erythrinidae). Front Genet 2018; 9:71. [PMID: 29556249 PMCID: PMC5845122 DOI: 10.3389/fgene.2018.00071] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 02/16/2018] [Indexed: 11/13/2022] Open
Abstract
The Erythrinidae family (Teleostei: Characiformes) is a small Neotropical fish group with a wide distribution throughout South America, where Hoplias malabaricus corresponds to the most widespread and cytogenetically studied taxon. This species possesses significant genetic variation, as well as huge karyotype diversity among populations, as reflected by its seven major karyotype forms (i.e., karyomorphs A-G) identified up to now. Although morphological differences in their bodies are not outstanding, H. malabaricus karyomorphs are easily identified by differences in 2n, morphology and size of chromosomes, as well as by distinct evolutionary steps of sex chromosomes development. Here, we performed comparative genomic hybridization (CGH) to analyse both the intra- and inter-genomic status in terms of repetitive DNA divergence among all but one (E) H. malabaricus karyomorphs. Our results indicated that they have close relationships, but with evolutionary divergences among their genomes, yielding a range of non-overlapping karyomorph-specific signals. Besides, male-specific regions were uncovered on the sex chromosomes, confirming their differential evolutionary trajectories. In conclusion, the hypothesis that H. malabaricus karyomorphs are result of speciation events was strengthened.
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Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czechia
| | - Luiz A. C. Bertollo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czechia
| | - Cassia F. Yano
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Ezequiel A. de Oliveira
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
- Secretaria de Estado de Educação de Mato Grosso (SEDUC-MT), Cuiabá, Brazil
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Perazzo GX, Noleto RB, Vicari MR, Gava A, Cestari MM. B chromosome polymorphism in South American cichlid. NEOTROPICAL BIODIVERSITY 2018. [DOI: 10.1080/23766808.2018.1429164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
| | - Rafael Bueno Noleto
- Department of Biology, State University of Paraná, União da Vitória, Paraná, Brazil
| | - Marcelo Ricardo Vicari
- Department of Structural, Molecular and Genetical Biology, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Adriana Gava
- Biological Sciences Institute, Federal University of Rio Grande, Rio Grande, Brazil
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Majtánová Z, Choleva L, Symonová R, Ráb P, Kotusz J, Pekárik L, Janko K. Asexual Reproduction Does Not Apparently Increase the Rate of Chromosomal Evolution: Karyotype Stability in Diploid and Triploid Clonal Hybrid Fish (Cobitis, Cypriniformes, Teleostei). PLoS One 2016; 11:e0146872. [PMID: 26808475 PMCID: PMC4726494 DOI: 10.1371/journal.pone.0146872] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 12/25/2015] [Indexed: 12/23/2022] Open
Abstract
Interspecific hybridization, polyploidization and transitions from sexuality to asexuality considerably affect organismal genomes. Especially the last mentioned process has been assumed to play a significant role in the initiation of chromosomal rearrangements, causing increased rates of karyotype evolution. We used cytogenetic analysis and molecular dating of cladogenetic events to compare the rate of changes of chromosome morphology and karyotype in asexually and sexually reproducing counterparts in European spined loach fish (Cobitis). We studied metaphases of three sexually reproducing species and their diploid and polyploid hybrid clones of different age of origin. The material includes artificial F1 hybrid strains, representatives of lineage originated in Holocene epoch, and also individuals of an oldest known age to date (roughly 0.37 MYA). Thereafter we applied GISH technique as a marker to differentiate parental chromosomal sets in hybrids. Although the sexual species accumulated remarkable chromosomal rearrangements after their speciation, we observed no differences in chromosome numbers and/or morphology among karyotypes of asexual hybrids. These hybrids possess chromosome sets originating from respective parental species with no cytogenetically detectable recombinations, suggesting their integrity even in a long term. The switch to asexual reproduction thus did not provoke any significant acceleration of the rate of chromosomal evolution in Cobitis. Asexual animals described in other case studies reproduce ameiotically, while Cobitis hybrids described here produce eggs likely through modified meiosis. Therefore, our findings indicate that the effect of asexuality on the rate of chromosomal change may be context-dependent rather than universal and related to particular type of asexual reproduction.
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Affiliation(s)
- Zuzana Majtánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, CAS, v.v.i, Liběchov, Czech Republic
- Department of Zoology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- * E-mail:
| | - Lukáš Choleva
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, CAS, v.v.i, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Radka Symonová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, CAS, v.v.i, Liběchov, Czech Republic
- Research Institute for Limnology, University of Innsbruck, Mondsee, Austria
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, CAS, v.v.i, Liběchov, Czech Republic
| | - Jan Kotusz
- Museum of Natural History, University of Wrocław, Wrocław, Poland
| | - Ladislav Pekárik
- Institute of Botany, SAS, Bratislava, Slovakia
- Department of Biology, Faculty of Education, Trnava University, Trnava, Slovakia
| | - Karel Janko
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, CAS, v.v.i, Liběchov, Czech Republic
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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Younis A, Ramzan F, Hwang YJ, Lim KB. FISH and GISH: molecular cytogenetic tools and their applications in ornamental plants. PLANT CELL REPORTS 2015; 34:1477-1488. [PMID: 26123291 DOI: 10.1007/s00299-015-1828-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 06/15/2015] [Indexed: 06/04/2023]
Abstract
The innovations in chromosome engineering have improved the efficiency of interrogation breeding, and the identification and transfer of resistance genes from alien to native species. Recent advances in molecular biology and cytogenetics have brought revolutionary, conceptual developments in mitosis and meiosis research, chromosome structure and manipulation, gene expression and regulation, and gene silencing. Cytogenetic studies offer integrative tools for imaging, genetics, epigenetics, and cytological information that can be employed to enhance chromosome and molecular genomic research in plant taxa. In situ hybridization techniques, such as fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH), can identify chromosome morphologies and sequences, amount and distribution of various types of chromatin in chromosomes, and genome organization during the metaphase stage of meiosis. Over the past few decades, various new molecular cytogenetic applications have been developed. The FISH and GISH techniques present an authentic model for analyzing the individual chromosome, chromosomal segments, or the genomes of natural and artificial hybrid plants. These have become the most reliable techniques for studying allopolyploids, because most cultivated plants have been developed through hybridization or polyploidization. Moreover, introgression of the genes and chromatin from the wild types into cultivated species can also be analyzed. Since hybrid derivatives may have variable alien chromosome numbers or chromosome arms, the use of these approaches opens new avenues for accurately identifying genome differences.
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Affiliation(s)
- Adnan Younis
- Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, South Korea,
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Huang X, Bi K, Lu W, Wang S, Zhang L, Bao Z. Genomic in situ hybridization identifies parental chromosomes in hybrid scallop (Bivalvia, Pectinoida, Pectinidae) between female Chlamysfarreri and male Argopectenirradiansirradians. COMPARATIVE CYTOGENETICS 2015; 9:189-200. [PMID: 26140161 PMCID: PMC4488966 DOI: 10.3897/compcytogen.v9i2.8943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 04/07/2015] [Indexed: 06/04/2023]
Abstract
Interspecific crossing was artificially carried out between Chlamysfarreri (Jones & Preston, 1904) ♀ and Argopectenirradiansirradians (Lamarck, 1819) ♂, two of the dominant cultivated scallop species in China. Genomic in situ hybridization (GISH) was used to examine the chromosome constitution and variation in hybrids at early embryonic stage. The number of chromosomes in 66.38% of the metaphases was 2n = 35 and the karyotype was 2n = 3 m + 5 sm + 16 st + 11 t. After GISH, two parental genomes were clearly distinguished in hybrids, most of which comprised 19 chromosomes derived from their female parent (Chlamysfarreri) and 16 chromosomes from their male parent (Argopectenirradiansirradians). Some chromosome elimination and fragmentation was also observed in the hybrids.
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Affiliation(s)
- Xiaoting Huang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Ke Bi
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
- Museum of Vertebrate Zoology, University of California, Berkeley, California 94720, USA
| | - Wei Lu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Shi Wang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Lingling Zhang
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
| | - Zhenmin Bao
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao 266003, China
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Hodaňová L, Kalous L, Musilová Z. Comparative cytogenetics of Neotropical cichlid fishes (Nannacara, Ivanacara and Cleithracara) indicates evolutionary reduction of diploid chromosome numbers. COMPARATIVE CYTOGENETICS 2014; 8:169-83. [PMID: 25349669 PMCID: PMC4205487 DOI: 10.3897/compcytogen.v8i3.7279] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 07/29/2014] [Indexed: 06/01/2023]
Abstract
A comparative cytogenetic analysis was carried out in five species of a monophyletic clade of neotropical Cichlasomatine cichlids, namely Cleithracara maronii Steindachner, 1881, Ivanacara adoketa (Kullander & Prada-Pedreros, 1993), Nannacara anomala Regan, 1905, N. aureocephalus Allgayer, 1983 and N. taenia Regan, 1912. Karyotypes and other chromosomal characteristics were revealed by CDD banding and mapped onto the phylogenetic hypothesis based on molecular analyses of four genes, namely cyt b, 16S rRNA, S7 and RAG1. The diploid numbers of chromosomes ranged from 44 to 50, karyotypes were composed predominantly of monoarmed chromosomes and one to three pairs of CMA3 signal were observed. The results showed evolutionary reduction in this monophyletic clade and the cytogenetic mechanisms (fissions/fusions) were hypothesized and discussed.
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Affiliation(s)
- Lucie Hodaňová
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Lukáš Kalous
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Zuzana Musilová
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics AV CR, Libechov, Czech Republic
- Zoological Institute, University of Basel, Switzerland
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Symonová R, Flajšhans M, Sember A, Havelka M, Gela D, Kořínková T, Rodina M, Rábová M, Ráb P. Molecular cytogenetics in artificial hybrid and highly polyploid sturgeons: An evolutionary story narrated by repetitive sequences. Cytogenet Genome Res 2013; 141:153-62. [PMID: 24051427 DOI: 10.1159/000354882] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We applied comparative genomic hybridization (CGH) and genomic in situ hybridization (GISH) to examine genomes of artificially produced sturgeon hybrids between sterlet, Acipenser ruthenus female (∼120 chromosomes) or Russian sturgeon, A. gueldenstaedtii female (∼240 chromosomes) and a spontaneous triploid Siberian sturgeon A. baerii male (∼360 chromosomes), respectively. The ploidy levels of progenies were analyzed by karyotyping and flow cytometry. We found that the species-specific regions were surprisingly identifiable only on some micro- and small(er) macrochromosomes in hybrid metaphases. We hypothesize that these distinguishable regions are represented by species-specific repetitive sequences driven by more dynamic molecular evolutionary mechanisms. On larger chromosomes, GISH faintly visualized only blocks of pericentromeric and telomeric repetitive sequences, remaining regions were equally shared by both parental species. We concluded that the interspecies hybridization producing viable and even fertile progeny is enabled by the fact that genomes of the species involved are likely divergent at the level of the repetitive sequences only and probably highly conserved in the coding sequences. These small differences of coding sequences are in concordance with previous estimations of relatedness of examined species producing artificial as well as natural hybrids. CGH and GISH represent a challenge in sturgeon cytogenetics as a valuable though technically not simple tool to discriminate chromosomes of parental species in hybrids. The potentials and drawbacks of CGH and GISH application in sturgeons are discussed and further experimental possibilities are proposed.
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Affiliation(s)
- R Symonová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Liběchov, Czech Republic
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11
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Hu L, Huang X, Mao J, Wang C, Bao Z. Genomic characterization of interspecific hybrids between the scallops Argopecten purpuratus and A. irradians irradians. PLoS One 2013; 8:e62432. [PMID: 23620828 PMCID: PMC3631176 DOI: 10.1371/journal.pone.0062432] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/21/2013] [Indexed: 11/19/2022] Open
Abstract
The Peruvian scallop (Argopecten purpuratus) has been introduced to China and has successfully been hybridized with the bay scallop (A. irradians irradians). The F1 hybrids of these two scallops exhibited a large increase in production traits and some other interesting new characteristics. To understand the genetic basis of this heterosis, nuclear gene and partial mtDNA sequences, and genomic in situ hybridization (GISH) were employed to analyze the genomic organization of the hybrids. Amplification of the ribosomal DNA internal transcribed spacer (ITS) showed that the parental ITS sequences were present in all the hybrid individuals, illustrating that the hybrid offspring inherited nuclear DNA from both parents. Sequence analyses of the ITS region further confirmed that the hybrids harbored alleles from their parents; some recombinant variants were also detected, which revealed some alterations in the nuclear genetic material of the hybrids. The analysis of mitochondrial 16S rDNA showed that the hybrids possessed sequences that were identical to the 16S rDNA of the female parents, proving a matrilineal inheritance of mitochondrial genes in scallops. In addition, GISH clearly discriminated between the parental chromosomes and indicated a combination of haploid genomes of duplex parents in the hybrids. The genetic analyses in our study illustrated that the F1 hybrids inherited nuclear material from both parents and cytoplasmic genetic material maternally, and some variations occurred in the genome, which might contribute to a further understanding of crossbreeding and heterosis in scallop species.
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Affiliation(s)
- Liping Hu
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Huang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- * E-mail:
| | - Junxia Mao
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chunde Wang
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Zhenmin Bao
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
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Mazzuchelli J, Kocher TD, Yang F, Martins C. Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish. BMC Genomics 2012; 13:463. [PMID: 22958299 PMCID: PMC3463429 DOI: 10.1186/1471-2164-13-463] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 08/09/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The availability of a large number of recently sequenced vertebrate genomes opens new avenues to integrate cytogenetics and genomics in comparative and evolutionary studies. Cytogenetic mapping can offer alternative means to identify conserved synteny shared by distinct genomes and also to define genome regions that are still not fine characterized even after wide-ranging nucleotide sequence efforts. An efficient way to perform comparative cytogenetic mapping is based on BAC clones mapping by fluorescence in situ hybridization. In this report, to address the knowledge gap on the genome evolution in cichlid fishes, BAC clones of an Oreochromis niloticus library covering the linkage groups (LG) 1, 3, 5, and 7 were mapped onto the chromosomes of 9 African cichlid species. The cytogenetic mapping data were also integrated with BAC-end sequences information of O. niloticus and comparatively analyzed against the genome of other fish species and vertebrates. RESULTS The location of BACs from LG1, 3, 5, and 7 revealed a strong chromosomal conservation among the analyzed cichlid species genomes, which evidenced a synteny of the markers of each LG. Comparative in silico analysis also identified large genomic blocks that were conserved in distantly related fish groups and also in other vertebrates. CONCLUSIONS Although it has been suggested that fishes contain plastic genomes with high rates of chromosomal rearrangements and probably low rates of synteny conservation, our results evidence that large syntenic chromosome segments have been maintained conserved during evolution, at least for the considered markers. Additionally, our current cytogenetic mapping efforts integrated with genomic approaches conduct to a new perspective to address important questions involving chromosome evolution in fishes.
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Affiliation(s)
- Juliana Mazzuchelli
- Department of Morphology, Bioscience Institute, UNESP - São Paulo State University, 18618-970, Botucatu, SP, Brazil
| | | | - Fengtang Yang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Cesar Martins
- Department of Morphology, Bioscience Institute, UNESP - São Paulo State University, 18618-970, Botucatu, SP, Brazil
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13
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Rampin M, Bi K, Bogart JP, Collares-Pereira MJ. Identifying parental chromosomes and genomic rearrangements in animal hybrid complexes of species with small genome size using Genomic In Situ Hybridization (GISH). COMPARATIVE CYTOGENETICS 2012; 6:287-300. [PMID: 24260669 PMCID: PMC3833804 DOI: 10.3897/compcytogen.v6i3.3543] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2012] [Accepted: 08/09/2012] [Indexed: 05/13/2023]
Abstract
Genomic In Situ Hybridization (GISH) is a powerful tool to identify and to quantify genomic constituents in allopolyploids, and is mainly based on hybridization of highly and moderate repetitive sequences. In animals, as opposed to plants, GISH has not been widely used in part because there are technical problems in obtaining informative results. Using the allopolyploid Squalius alburnoides Steindachner, 1866 fish complex as a model system, we succeeded in overcoming methodological constraints when dealing with parental species with a small genome size. This hybridogenetic complex has biotypes with different genome compositions and ploidy levels, but parental chromosomes are small, morphologically very similar and therefore cannot be distinguished by conventional cytogenetic approaches. Specimens have a small genome (C-value1.2 pg) with a low level of highly and moderate repetitive sequences, mainly located at pericentromeric chromosome regions. Since it is well known that probe annealing depends on probe concentration and hybridization time to obtain uniform hybridization signals along the chromosome arms, we progressively increased the amount of labeled probes from 100ng up to 1µg and the incubation time from overnight up to 5 days. We also made other smaller improvements. Results showed a clear enhancement of signals with respect to previous data, allowing an accurate and reproducible assignment of the parental genomes in both diploid and triploid fish.It was thus evidenced that high probes' concentrations and long incubation time are the key to obtain, without extra image editing, uniform and reliable hybridization signals in metaphase chromosomes of animal hybrids from species with small genome size.
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Affiliation(s)
- Massimiliano Rampin
- Centro de Biologia Ambiental - Faculdade de Ciências - Universidade de Lisboa, Campo Grande - 1749-016 Lisboa, Portugal
| | - Ke Bi
- Department of Integrative Biology, University of Guelph, Guelph, Ontario (Canada)
| | - James P. Bogart
- Museum of Vertebrate Zoology, University of California, Berkeley, California (USA)
| | - Maria João Collares-Pereira
- Centro de Biologia Ambiental - Faculdade de Ciências - Universidade de Lisboa, Campo Grande - 1749-016 Lisboa, Portugal
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14
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Huang X, Bi K, Hu L, Sun Y, Lu W, Bao Z. Fertilization and cytogenetic examination of interspecific reciprocal hybridization between the scallops, Chlamys farreri and Mimachlamys nobilis. PLoS One 2011; 6:e27235. [PMID: 22110617 PMCID: PMC3215693 DOI: 10.1371/journal.pone.0027235] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 10/12/2011] [Indexed: 11/18/2022] Open
Abstract
Crossbreeding is a powerful tool for improving productivity and profitability in aquaculture. We conducted a pilot study of an artificial cross between two important cultivated scallops in China, Chlamys farreri and Mimachlamys nobilis, to test the feasibility of interspecific hybridization. Reciprocal hybridization experiments were performed using a single-pair mating strategy (M. nobilis ♀ × C. farreri ♂ and C. farreri ♀ × M. nobilis ♂). The fertilization of each pair was tracked using fluorescence staining of the gametes, and the chromosomes of the F1 hybrid larvae were examined via conventional karyotyping and genomic in situ hybridization (GISH). We observed moderate fertilization success in both interspecific crosses, although the overall fertilization was generally less rapid than that of intraspecific crosses. Conventional karyotyping showed that 70.4% of the viable F1 larvae in M. nobilis ♀ × C. farreri ♂ and 55.4% in C. farreri ♀ × M. nobilis ♂ comprised hybrid karyotypes (2n = 35 = 6m+5sm+11st+13t), and the results were further confirmed by GISH. Interestingly, we detected a few F1 from the M. nobilis ♀ × C. farreri ♂ cross that appeared to have developed gynogenetically. In addition, chromosome fragmentations, aneuploids and allopolyploids were observed in some F1 individuals. Our study presents evidence that the artificial cross between M. nobilis and C. farreri is experimentally possible. Further investigations of the potential heterosis of the viable F1 offspring at various developmental stages should be conducted to obtain a comprehensive evaluation of the feasibility of crossbreeding between these two scallop species.
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Affiliation(s)
- Xiaoting Huang
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
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15
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Zaleśna A, Choleva L, Ogielska M, Rábová M, Marec F, Ráb P. Evidence for integrity of parental genomes in the diploid hybridogenetic water frog Pelophylax esculentus by genomic in situ hybridization. Cytogenet Genome Res 2011; 134:206-12. [PMID: 21555873 DOI: 10.1159/000327716] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2011] [Indexed: 11/19/2022] Open
Abstract
The Western Palearctic water frogs Pelophylax ridibundus and P. lessonae were identified as parental (sexual) species and P. esculentus as their interspecific, hybridogenetically reproducing hybrid with hemiclonal heredity. We used genomic in situ hybridization (GISH) to identify parental chromosomes of P.lessonae and P.ridibundus in diploid P. esculentus karyotypes (2n = 26). GISH probes were made by fluorochrome labeling of total genomic DNA extracted from the sexual progenitors. The labeled probe from one species was hybridized to chromosomes of P. esculentus in the presence of excess of unlabeled genomic DNA from the other species. Thus, the P. lessonae probe was blocked by P. ridibundus unlabeled DNA, and vice versa. We successfully discriminated each of the 13 respective parental chromosomes in metaphase complements of the hybrids according to species-specific hybridization signals. GISH enabled us to confirm additional differences between parental chromosomes in size (smaller chromosomes belong to P. lessonae) and in the presence of DAPI-positive centromeric heterochromatin (detected in chromosomes of P. ridibundus, but not in P. lessonae). The fact that no visible intergenomic exchanges were found in metaphase chromosomes of diploid P. esculentus provides important information on the genomic integrity of hemiclonal transmission and supports hybridogenesis as a reproductive mode at the chromosome level for the specimens examined.
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Affiliation(s)
- A Zaleśna
- Department of Biology and Conservation of Vertebrates, Zoological Institute, University of Wroclaw, Wroclaw, Poland
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16
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Valente G, Mazzuchelli J, Ferreira I, Poletto A, Fantinatti B, Martins C. Cytogenetic Mapping of the Retroelements Rex1, Rex3 and Rex6 among Cichlid Fish: New Insights on the Chromosomal Distribution of Transposable Elements. Cytogenet Genome Res 2011; 133:34-42. [DOI: 10.1159/000322888] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2010] [Indexed: 11/19/2022] Open
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Ferreira I, Poletto A, Kocher T, Mota-Velasco J, Penman D, Martins C. Chromosome evolution in African cichlid fish: contributions from the physical mapping of repeated DNAs. Cytogenet Genome Res 2010; 129:314-22. [PMID: 20606399 PMCID: PMC3202915 DOI: 10.1159/000315895] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2010] [Indexed: 01/25/2023] Open
Abstract
Cichlid fishes have been the subject of increasing scientific interest because of their rapid adaptive radiation that has led to extensive ecological diversity and because of their enormous importance to tropical and subtropical aquaculture. To further understanding of chromosome evolution among cichlid species, we have comparatively mapped the SATA satellite DNA, the transposable element ROn-1, and repeated sequences in the bacterial artificial chromosome clone BAC-C4E09 on the chromosomes of a range of African species of Cichlidae, using fluorescence in situ hybridization. The SATA satellite DNA was mapped in almost all the centromeres of all tilapiine and haplochromine species studied. The maintenance and centromeric distribution of the SATA satellite DNA in African cichlids suggest that this sequence plays an important role in the organization and function of the centromere in these species. Furthermore, analysis of SATA element distribution clarifies that chromosome fusions occurred independently in Oreochromis and Tilapia genera, and led to the reduced chromosome number detected in O. karongae and T. mariae. The comparative chromosome mapping of the ROn-1 SINE-like element and BAC-C4E09 shows that the repeated sequences have been maintained among tilapiine, haplochromine and hemichromine fishes and has demonstrated the homology of the largest chromosomes among these groups. Furthermore, the mapping of ROn-1 suggested that different chromosomal rearrangements could have occurred in the origin of the largest chromosome pairs of tilapiines and non-tilapiines.
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Affiliation(s)
- I.A. Ferreira
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - A.B. Poletto
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
| | - T.D. Kocher
- Department of Biology, University of Maryland, College Park, Md., USA
| | - J.C. Mota-Velasco
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
| | - D.J. Penman
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, UK
| | - C. Martins
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista, Botucatu, Brazil
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