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Menezes RST, Cabral-de-Mello DC, Milani D, Bardella VB, Almeida EAB. The relevance of chromosome fissions for major ribosomal DNA dispersion in hymenopteran insects. J Evol Biol 2021; 34:1466-1476. [PMID: 34331340 DOI: 10.1111/jeb.13909] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 07/04/2021] [Accepted: 07/28/2021] [Indexed: 01/20/2023]
Abstract
Ribosomal DNA (rDNA) loci are essential for cellular metabolism due to their participation in ribosome biogenesis. Although these genes have been widely cytogenetically mapped, the evolutionary mechanisms behind their variability in number and chromosomal location remain elusive, even in well-known biological groups, such as ants, bees and wasps (Insecta: Hymenoptera). To address this question in Hymenoptera and therefore advance the understanding of rDNA evolution in insects in general, we integrated molecular cytogenetic data, a phylogenomic framework, model-based predictions and genome sequencing. Hence, we assessed the main evolutionary trends shaping the chromosomal distribution of rDNA loci in Hymenoptera. We noticed the conservation of one site of rDNA per haploid genome, suggesting that a single 45S rDNA locus is the putative ancestral pattern for aculeate Hymenoptera. Moreover, our results highlighted a nonrandom distribution of rDNA in Hymenoptera karyotypes, as well as a lineage-specific preferential location. The proximal location of rDNA is favoured in species with multiple loci and in the two families of Hymenoptera that show the highest range of chromosome numbers: Formicidae and Vespidae. We propose that chromosome fissions have played a crucial role in the distribution pattern of rDNA loci through the evolutionary diversification of Hymenoptera. Moreover, our genomic analysis of two species, one with a single locus of rDNA and one with multiple loci, supported that loci multiplication is followed by sequence divergence. Our results provide detailed information about the number and chromosomal position of rDNA in Hymenoptera and, therefore, broaden our knowledge regarding rDNA evolutionary dynamics in insects.
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Affiliation(s)
- Rodolpho S T Menezes
- Laboratório de Biologia Comparada e Abelhas, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras (FFCLRP), Universidade de São Paulo (USP), Ribeirão Preto, Brazil
| | - Diogo C Cabral-de-Mello
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Diogo Milani
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Vanessa B Bardella
- Departamento de Biologia Geral e Aplicada, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Rio Claro, Brazil
| | - Eduardo A B Almeida
- Laboratório de Biologia Comparada e Abelhas, Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras (FFCLRP), Universidade de São Paulo (USP), Ribeirão Preto, Brazil
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Elizeu AM, Travenzoli NM, de Paiva Ferreira R, Lopes DM, Tavares MG. Comparative study on the physical mapping of ribosomal genes and repetitive sequences in Friesella schrottkyi (Friese 1900) (Hymenoptera: Apidae, Meliponini). ZOOL ANZ 2021. [DOI: 10.1016/j.jcz.2021.04.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Cao L, Zhao C, Wang C, Qin H, Qin Q, Tao M, Zhang C, Zhao R, Liu S. Evolutionary dynamics of 18S and 5S rDNA in autotriploid Carassius auratus. Gene 2020; 737:144433. [PMID: 32014563 DOI: 10.1016/j.gene.2020.144433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023]
Abstract
The Carassius auratus (crucian carp) complex of the Dongting water system exhibits coexistence of diploid and triploid forms. As reported, triploid C. auratus is autotriploid origin. Ribosomal DNA (rDNA) with evolutionary conservation is widely used to study polyploidization. Here, we investigated genomic and transcribed rDNA sequences (18S and 5S) in diploid (2nCC, 2n = 100) and triploid (3nCC, 3n = 150) C. auratus. The results showed that the genetic traits and expression of 18S and 5S rDNA from 2nCC individuals were identified in 3nCC individuals. Moreover, pseudogenization of rDNA (18S and 5S) sequences were also observed in both 2nCC and 3nCC individuals, but expression of these variants was not detected. Based on the transcribed rDNA consensus sequence between 2nCC and 3nCC individuals, the functional secondary structures of 18S rRNA (expansion segments, ES6S) and 5S rRNA were predicted. These data demonstrated that complex evolutionary dynamics existed in the rDNA family of C. auratus. The evolutionary conservation of rDNA revealed that autotriploidization could not induce the divergence in Carassius taxa of the Dongting water system. These observations will expand our knowledge of the evolutionary dynamics of the rDNA family in vertebrates.
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Affiliation(s)
- Liu Cao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Chun Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Chongqing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Huan Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Rurong Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha 410081, Hunan, PR China; College of Life Sciences, Hunan Normal University, Changsha 410081, Hunan, PR China.
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Sember A, Pelikánová Š, de Bello Cioffi M, Šlechtová V, Hatanaka T, Do Doan H, Knytl M, Ráb P. Taxonomic Diversity Not Associated with Gross Karyotype Differentiation: The Case of Bighead Carps, Genus Hypophthalmichthys (Teleostei, Cypriniformes, Xenocyprididae). Genes (Basel) 2020; 11:E479. [PMID: 32354012 PMCID: PMC7291238 DOI: 10.3390/genes11050479] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 03/31/2020] [Accepted: 04/24/2020] [Indexed: 11/30/2022] Open
Abstract
The bighead carps of the genus Hypophthalmichthys (H. molitrix and H. nobilis) are important aquaculture species. They were subjected to extensive multidisciplinary research, but with cytogenetics confined to conventional protocols only. Here, we employed Giemsa-/C-/CMA3- stainings and chromosomal mapping of multigene families and telomeric repeats. Both species shared (i) a diploid chromosome number 2n = 48 and the karyotype structure, (ii) low amount of constitutive heterochromatin, (iii) the absence of interstitial telomeric sites (ITSs), (iv) a single pair of 5S rDNA loci adjacent to one major rDNA cluster, and (v) a single pair of co-localized U1/U2 snDNA tandem repeats. Both species, on the other hand, differed in (i) the presence/absence of remarkable interstitial block of constitutive heterochromatin on the largest acrocentric pair 11 and (ii) the number of major (CMA3-positive) rDNA sites. Additionally, we applied here, for the first time, the conventional cytogenetics in H. harmandi, a species considered extinct in the wild and/or extensively cross-hybridized with H. molitrix. Its 2n and karyotype description match those found in the previous two species, while silver staining showed differences in distribution of major rDNA. The bighead carps thus represent another case of taxonomic diversity not associated with gross karyotype differentiation, where 2n and karyotype structure cannot help in distinguishing between genomes of closely related species. On the other hand, we demonstrated that two cytogenetic characters (distribution of constitutive heterochromatin and major rDNA) may be useful for diagnosis of pure species. The universality of these markers must be further verified by analyzing other pure populations of bighead carps.
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Affiliation(s)
- Alexandr Sember
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277-21 Liběchov, Czech Republic
| | - Šárka Pelikánová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277-21 Liběchov, Czech Republic
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, São Carlos 13565-905, Brazil
| | - Vendula Šlechtová
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277-21 Liběchov, Czech Republic
| | - Terumi Hatanaka
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, Rod. Washington Luiz km 235 cep, São Carlos 13565-905, Brazil
| | - Hiep Do Doan
- Research Institute of Aquaculture No. 1, Dinh Bang, Tu Son, Bac Ninh 16000, Vietnam
| | - Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, 2-128-43 Prague, Czech Republic
| | - Petr Ráb
- Laboratory of Fish Genetics, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburská 89, 277-21 Liběchov, Czech Republic
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Maroso F, Pérez de Gracia C, Iglesias D, Cao A, Díaz S, Villalba A, Vera M, Martínez P. A Useful SNP Panel to Distinguish Two Cockle Species, Cerastoderma edule and C. glaucum, Co-Occurring in Some European Beds, and Their Putative Hybrids. Genes (Basel) 2019; 10:genes10100760. [PMID: 31569787 PMCID: PMC6826453 DOI: 10.3390/genes10100760] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 11/16/2022] Open
Abstract
Cockles are highly appreciated mollusks and provide important services in coastal areas. The two European species, edible (Cerastoderma edule) and lagoon (Cerastoderma glaucum) cockles, are not easily distinguishable, especially when young. Interestingly, the species show different resistance to Marteilia cochillia, the parasite responsible for marteiliosis outbreaks, which is devastating cockle production in some areas. C. edule is severely affected by the parasite, while C. glaucum seems to be resistant, although underlying reasons are still unknown. Hybrids between both species might be interesting to introgress allelic variants responsible for tolerance, either naturally or through artificial selection, from lagoon into edible cockle. Here, we used 2b restriction site-associated DNA sequencing (2b–RAD) to identify single nucleotide polymorphisms (SNP) diagnostic for cockle discrimination (fixed for alternative allelic variants). Among the nine diagnostic SNPs selected, seven were validated using a SNaPshot assay in samples covering most of the distribution range of both species. The validated SNPs were used to check cockles that were suggested to be hybrids by a claimed diagnostic tool based on the internal transcribed spacers of the ribosomal RNA. Although these were shown to be false positives, we cannot rule out the fact that hybrids can occur and be viable. The SNP tool here developed will be valuable for their identification and management.
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Affiliation(s)
- Francesco Maroso
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002 Lugo, Spain; (F.M.); (C.P.d.G.); (P.M.)
| | - Celia Pérez de Gracia
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002 Lugo, Spain; (F.M.); (C.P.d.G.); (P.M.)
| | - David Iglesias
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain; (D.I.); (A.C.); (A.V.)
| | - Asunción Cao
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain; (D.I.); (A.C.); (A.V.)
| | - Seila Díaz
- Department of Zoology, Genetics and Physical Anthropology, Mobile Genomes and Disease Group, CIMUS, Universidade de Santiago de Compostela, Campus of Santiago de Compostela, 15706 Santiago de Compostela, Spain;
| | - Antonio Villalba
- Centro de Investigacións Mariñas (CIMA), Consellería do Mar, Xunta de Galicia, 36620 Vilanova de Arousa, Spain; (D.I.); (A.C.); (A.V.)
- Department of Life Sciences, University of Alcalá, 28871 Alcalá de Henares, Spain
- Research Centre for Experimental Marine Biology and Biotechnology (PIE), University of the Basque Country (UPV/EHU), 48620 Plentzia, Basque Country, Spain
| | - Manuel Vera
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002 Lugo, Spain; (F.M.); (C.P.d.G.); (P.M.)
- Instituto de Acuicultura, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
- Correspondence: ; Tel.: +34-982-82-24-26
| | - Paulino Martínez
- Department of Zoology, Genetics and Physical Anthropology, ACUIGEN Group, Faculty of Veterinary, Universidade de Santiago de Compostela, Campus of Lugo, 27002 Lugo, Spain; (F.M.); (C.P.d.G.); (P.M.)
- Instituto de Acuicultura, Universidade de Santiago de Compostela, 15705 Santiago de Compostela, Spain
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How dynamic could be the 45S rDNA cistron? An intriguing variability in a grasshopper species revealed by integration of chromosomal and genomic data. Chromosoma 2019; 128:165-175. [DOI: 10.1007/s00412-019-00706-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/25/2019] [Accepted: 04/29/2019] [Indexed: 10/26/2022]
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Menezes RST, Gazoni T, Costa MA. Cytogenetics of warrior wasps (Vespidae:Synoeca) reveals intense evolutionary dynamics of ribosomal DNA clusters and an unprecedented number of microchromosomes in Hymenoptera. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Rodolpho S T Menezes
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras – Universidade de São Paulo (FFCLRP/USP), Ribeirão Preto, SP, Brazil
| | - Thiago Gazoni
- Departamento de Biologia – Universidade Estadual Paulista (UNESP), Instituto de Biociências, Rio Claro, SP, Brazil
| | - Marco A Costa
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
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Sochorová J, Garcia S, Gálvez F, Symonová R, Kovařík A. Evolutionary trends in animal ribosomal DNA loci: introduction to a new online database. Chromosoma 2018; 127:141-150. [PMID: 29192338 PMCID: PMC5818627 DOI: 10.1007/s00412-017-0651-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 11/06/2017] [Accepted: 11/07/2017] [Indexed: 11/24/2022]
Abstract
Ribosomal DNA (rDNA) loci encoding 5S and 45S (18S-5.8S-28S) rRNAs are important components of eukaryotic chromosomes. Here, we set up the animal rDNA database containing cytogenetic information about these loci in 1343 animal species (264 families) collected from 542 publications. The data are based on in situ hybridisation studies (both radioactive and fluorescent) carried out in major groups of vertebrates (fish, reptiles, amphibians, birds, and mammals) and invertebrates (mostly insects and mollusks). The database is accessible online at www.animalrdnadatabase.com . The median number of 45S and 5S sites was close to two per diploid chromosome set for both rDNAs despite large variation (1-74 for 5S and 1-54 for 45S sites). No significant correlation between the number of 5S and 45S rDNA loci was observed, suggesting that their distribution and amplification across the chromosomes follow independent evolutionary trajectories. Each group, irrespective of taxonomic classification, contained rDNA sites at any chromosome location. However, the distal and pericentromeric positions were the most prevalent (> 75% karyotypes) for 45S loci, while the position of 5S loci was more variable. We also examined potential relationships between molecular attributes of rDNA (homogenisation and expression) and cytogenetic parameters such as rDNA positions, chromosome number, and morphology.
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Affiliation(s)
- Jana Sochorová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, CZ-61265, Brno, Czech Republic
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Francisco Gálvez
- Bioscripts-Centro de Investigación y Desarrollo de Recursos Científicos, 41012, Sevilla, Andalusia, Spain
| | - Radka Symonová
- Faculty of Science, University of Hradec Kralove, Hradecka 1285, CZ-50003, Hradec Kralove, Czech Republic
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, CZ-61265, Brno, Czech Republic.
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Han CC, Yen TB, Chen NC, Tseng MC. Cytogenetics of Two Onychostoma Species in Taiwan by Ag-NOR and 18S rDNA Profiles. Zool Stud 2017; 56:e25. [PMID: 31966224 PMCID: PMC6517726 DOI: 10.6620/zs.2017.56-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/05/2017] [Indexed: 11/18/2022]
Abstract
Chiao-Chuan Han, Tsair-Bor Yen, Nian-Cih Chen, and Mei-Chen Tseng (2017) Both Onychostoma barbatulum and O. alticorpus are primary freshwater fish in Taiwan. The former has been developed as an aquaculture species with high economic value, while the latter is a native endemic species in Taiwan. Understanding the cytogenetic information of these two species is necessary for their selected breeding, recovery, and management. In this study, Giemsa staining, silver-binding nucleolar organizer region (Ag-NOR), C-banding, and fluorescence in situ hybridization (FISH) with 18S ribosomal (r)DNA probes were used to analyze the cytogenetic characteristics. Results of Giemsa staining showed that the two Onychostoma species shared the same number of chromosomes, 2n = 50. Respective karyotype formulas of the female and male were 10 m + 22 sm + 10 st + 8 t and 11 m + 22 sm + 10 st + 7 t in O. barbatulum, and 14 m + 18 sm + 8 st + 10 t and 15 m + 18 sm + 8 st + 9 t in O. alticorpus. Karyotypes of both species showed a pair of heteromorphic chromosomes in male fish. Their sex determination should be the XX/XY system. Two pairs of Ag-NORs were found in O. barbatulum, but only one pair occurred in O. alticorpus. C-banding areas were observed on centromeres or telomeres of some chromosomes. FISH revealed different cytogenetic characters between these two species. The above cytogenetic information will contribute to species identification, population recovery, and advantages for breeding and management in the future.
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Affiliation(s)
- Chiao-Chuan Han
- National Museum of Marine Biology and Aquarium, Pingtung 944, Taiwan. E-mail:
- Graduate Institute of Marine Biology, National Dong Hwa University, Hualien 974, Taiwan
| | - Tsair-Bor Yen
- Department of Tropical Agriculture and International Cooperation, National Pingtung
University of Science and Technology, Pingtung 912, Taiwan. E-mail:
| | - Nian-Cih Chen
- Department of Aquaculture, National Pingtung University of Science and Technology,
Pingtung 912, Taiwan
| | - Mei-Chen Tseng
- Department of Aquaculture, National Pingtung University of Science and Technology,
Pingtung 912, Taiwan
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Jetybayev IY, Bugrov AG, Ünal M, Buleu OG, Rubtsov NB. Molecular cytogenetic analysis reveals the existence of two independent neo-XY sex chromosome systems in Anatolian Pamphagidae grasshoppers. BMC Evol Biol 2017; 17:20. [PMID: 28251879 PMCID: PMC5333169 DOI: 10.1186/s12862-016-0868-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Neo-XY sex chromosome determination is a rare event in short horned grasshoppers, but it appears with unusual frequency in the Pamphagidae family. The neo-Y chromosomes found in several species appear to have undergone heterochromatinization and degradation, but this subject needs to be analyzed in other Pamphagidae species. We perform here karyotyping and molecular cytogenetic analyses in 12 Pamphagidae species from the center of biodiversity of this group in the previously-unstudied Anatolian plateau. RESULTS The basal karyotype for the Pamphagidae family, consisting of 18 acrocentric autosomes and an acrocentric X chromosome (2n♂ = 19, X0; 2n♀ = 20, XX), was found only in G. adaliae. The karyotype of all other studied species consisted of 16 acrocentric autosomes and a neo-XY sex chromosome system (2n♂♀ = 18, neo-XX♀/neo-XY♂). Two different types of neo-Y chromosomes were found. One of them was typical for three species of the Glyphotmethis genus, and showed a neo-Y chromosome being similar in size to the XR arm of the neo-X, with the addition of two small subproximal interstitial C-blocks. The second type of the neo-Y chromosome was smaller and more heterochromatinized than the XR arm, and was typical for all Nocarodeini species studied. The chromosome distribution of C-positive regions and clusters of ribosomal DNA (rDNA) and telomeric repeats yielded additional information on evolution of these neo-XY systems. CONCLUSION Most Pamphagidae species in the Anatolian region were found to have neo-XY sex chromosome systems, belonging to two different evolutionary lineages, marked by independent X-autosome fusion events occurred within the Trinchinae and Pamphaginae subfamilies. The high density of species carrying neo-XY systems in the Anatolian region, and the different evolutionary stage for the two lineages found, one being older than the other, indicates that this region has a long history of neo-XY sex chromosome formation.
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Affiliation(s)
- Ilyas Yerkinovich Jetybayev
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Pr. Lavrentjeva 10, 630090, Novosibirsk, Russia. .,Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091, Novosibirsk, Russia.
| | - Alexander Gennadievich Bugrov
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091, Novosibirsk, Russia.,Novosibirsk State University, Pirogov str., 2, 630090, Novosibirsk, Russia
| | - Mustafa Ünal
- Fen-Edebiyat Fakültesi, Biyoloji Bölümü, Abant İzzet Baysal Üniversitesi, TR-14030, Bolu, Türkiye
| | - Olesya Georgievna Buleu
- Institute of Systematics and Ecology of Animals, Russian Academy of Sciences, Siberian Branch, Frunze str. 11, 630091, Novosibirsk, Russia.,Novosibirsk State University, Pirogov str., 2, 630090, Novosibirsk, Russia
| | - Nikolay Borisovich Rubtsov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Pr. Lavrentjeva 10, 630090, Novosibirsk, Russia.,Novosibirsk State University, Pirogov str., 2, 630090, Novosibirsk, Russia
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Kasiroek W, Indananda C, Pinthong K, Supiwong W, Pengseng P, Tanomtong A. NOR Polymorphism and Chromosome Analysis of Banggai Cardinalfish, Pterapogon kauderni (Perciformes, Apogonidae). CYTOLOGIA 2017. [DOI: 10.1508/cytologia.82.17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Wannapa Kasiroek
- Department of Aquatic Science, Faculty of Science, Burapha University
- Institute of Marine Science, Burapha University
| | | | - Krit Pinthong
- Department of Fundamental Science, Faculty of Science and Technology, Surindra Rajabhat University
| | | | - Puan Pengseng
- School of Agricultural of Technology, Walailak University
| | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology, Faculty of Science,
Khon Kaen University
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12
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Kasiroek W, Indananda C, Luangoon N, Pinthong K, Supiwong W, Tanomtong A. First Chromosome Analysis of the Humpback Cardinalfish, Fibramia lateralis (Perciformes, Apogonidae). CYTOLOGIA 2017. [DOI: 10.1508/cytologia.82.9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Wannapa Kasiroek
- Department of Aquatic Science, Faculty of Science, Burapha University
- Institute of Marine Science, Burapha University
| | | | | | - Krit Pinthong
- Department of Fundamental Science, Faculty of Science and Technology, Surindra Rajabhat University
| | | | - Alongklod Tanomtong
- Toxic Substances in Livestock and Aquatic Animals Research Group, Department of Biology,
Faculty of Science, Khon Kaen University
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Śliwińska-Jewsiewicka A, Kuciński M, Kirtiklis L, Dobosz S, Ocalewicz K, Jankun M. Chromosomal characteristics and distribution of rDNA sequences in the brook trout Salvelinus fontinalis (Mitchill, 1814). Genetica 2015; 143:425-32. [PMID: 25958180 PMCID: PMC4486110 DOI: 10.1007/s10709-015-9841-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 05/04/2015] [Indexed: 11/09/2022]
Abstract
Brook trout Salvelinus fontinalis (Mitchill, 1814) chromosomes have been analyzed using conventional and molecular cytogenetic techniques enabling characteristics and chromosomal location of heterochromatin, nucleolus organizer regions (NORs), ribosomal RNA-encoding genes and telomeric DNA sequences. The C-banding and chromosome digestion with the restriction endonucleases demonstrated distribution and heterogeneity of the heterochromatin in the brook trout genome. DNA sequences of the ribosomal RNA genes, namely the nucleolus-forming 28S (major) and non-nucleolus-forming 5S (minor) rDNAs, were physically mapped using fluorescence in situ hybridization (FISH) and primed in situ labelling. The minor rDNA locus was located on the subtelo-acrocentric chromosome pair No. 9, whereas the major rDNA loci were dispersed on 14 chromosome pairs, showing a considerable inter-individual variation in the number and location. The major and minor rDNA loci were located at different chromosomes. Multichromosomal location (3-6 sites) of the NORs was demonstrated by silver nitrate (AgNO3) impregnation. All Ag-positive i.e. active NORs corresponded to the GC-rich blocks of heterochromatin. FISH with telomeric probe showed the presence of the interstitial telomeric site (ITS) adjacent to the NOR/28S rDNA site on the chromosome 11. This ITS was presumably remnant of the chromosome rearrangement(s) leading to the genomic redistribution of the rDNA sequences. Comparative analysis of the cytogenetic data among several related salmonid species confirmed huge variation in the number and the chromosomal location of rRNA gene clusters in the Salvelinus genome.
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Affiliation(s)
- A. Śliwińska-Jewsiewicka
- />Department of Human Histology and Embryology, Faculty of Medical Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - M. Kuciński
- />Department of Ichthyology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - L. Kirtiklis
- />Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - S. Dobosz
- />Department of Salmonid Research, Inland Fisheries Institute in Olsztyn, Olsztyn, Poland
| | - K. Ocalewicz
- />Department of Marine Biology and Ecology, Faculty of Oceanography and Geography, University of Gdansk, Gdańsk, Poland
| | - Malgorzata Jankun
- />Department of Ichthyology, Faculty of Environmental Sciences, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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Pita S, Panzera F, Ferrandis I, Galvão C, Gómez-Palacio A, Panzera Y. Chromosomal divergence and evolutionary inferences in Rhodniini based on the chromosomal location of ribosomal genes. Mem Inst Oswaldo Cruz 2014; 108:S0074-02762013000300376. [PMID: 23778665 DOI: 10.1590/s0074-02762013000300017] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 02/07/2013] [Indexed: 11/22/2022] Open
Abstract
In this study, we used fluorescence in situ hybridisation to determine the chromosomal location of 45S rDNA clusters in 10 species of the tribe Rhodniini (Hemiptera: Reduviidae: Triatominae). The results showed striking inter and intraspecific variability, with the location of the rDNA clusters restricted to sex chromosomes with two patterns: either on one (X chromosome) or both sex chromosomes (X and Y chromosomes). This variation occurs within a genus that has an unchanging diploid chromosome number (2n = 22, including 20 autosomes and 2 sex chromosomes) and a similar chromosome size and genomic DNA content, reflecting a genome dynamic not revealed by these chromosome traits. The rDNA variation in closely related species and the intraspecific polymorphism in Rhodnius ecuadoriensis suggested that the chromosomal position of rDNA clusters might be a useful marker to identify recently diverged species or populations. We discuss the ancestral position of ribosomal genes in the tribe Rhodniini and the possible mechanisms involved in the variation of the rDNA clusters, including the loss of rDNA loci on the Y chromosome, transposition and ectopic pairing. The last two processes involve chromosomal exchanges between both sex chromosomes, in contrast to the widely accepted idea that the achiasmatic sex chromosomes of Heteroptera do not interchange sequences.
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Affiliation(s)
- Sebastián Pita
- Universidad de la República, Facultad de Ciencias, Sección Genética Evolutiva, Montevideo, Uruguay
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15
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Almeida JS, Affonso PRADM, Diniz D, Carneiro PLS, Dias AL. Chromosomal Variation in the Tropical Armored Catfish Callichthys Callichthys (Siluriformes, Callichthyidae): Implications for Conservation and Taxonomy in a Species Complex from a Brazilian Hotspot. Zebrafish 2013; 10:451-8. [DOI: 10.1089/zeb.2013.0885] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
| | | | - Débora Diniz
- Department of Biological Sciences, State University of Southwestern Bahia, Jequié, Brazil
| | | | - Ana Lúcia Dias
- Department of General Biology, State University of Londrina, Londrina, Brazil
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16
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Panzera Y, Pita S, Ferreiro MJ, Ferrandis I, Lages C, Pérez R, Silva AE, Guerra M, Panzera F. High Dynamics of rDNA Cluster Location in Kissing Bug Holocentric Chromosomes (Triatominae, Heteroptera). Cytogenet Genome Res 2012; 138:56-67. [PMID: 22907389 DOI: 10.1159/000341888] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2012] [Indexed: 11/19/2022] Open
Affiliation(s)
- Y Panzera
- Sección Genética Evolutiva, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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17
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Cabral-de-Mello DC, Cabrero J, López-León MD, Camacho JPM. Evolutionary dynamics of 5S rDNA location in acridid grasshoppers and its relationship with H3 histone gene and 45S rDNA location. Genetica 2011; 139:921-31. [PMID: 21755328 DOI: 10.1007/s10709-011-9596-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 07/01/2011] [Indexed: 10/18/2022]
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18
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Ocalewicz K, Woznicki P, Furgala-Selezniow G, Jankun M. Chromosomal location of Ag/CMA3-NORs, 5S rDNA and telomeric repeats in two stickleback species. ACTA ACUST UNITED AC 2011. [DOI: 10.1080/11250003.2010.532160] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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19
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Orosová M, Ivica KH, Eva B, Marta Š. Karyotype, chromosomal characteristics of multiple rDNA clusters and intragenomic variability of ribosomal ITS2 in Caryophyllaeides fennica (Cestoda). Parasitol Int 2010; 59:351-7. [DOI: 10.1016/j.parint.2010.04.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 04/27/2010] [Accepted: 04/28/2010] [Indexed: 11/30/2022]
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20
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Singh M, Kumar R, Nagpure NS, Kushwaha B, Mani I, Chauhan UK, Lakra WS. Population distribution of 45S and 5S rDNA in golden mahseer, Tor putitora: population-specific FISH marker. J Genet 2010; 88:315-20. [PMID: 20086297 DOI: 10.1007/s12041-009-0045-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Chromosomal locations of major 45S and minor 5S ribosomal DNAs (rDNAs) and organization of 5S rRNA genes were analysed in five different populations of golden mahseers (Tor putitora) using fluorescence in situ hybridization (FISH) and Southern blot hybridization. All five populations of T. putitora (2n = 100) showed a similar type of macro-karyotype composed of 12 metacentric, 22 submetacentric, 14 subtelocentric and 52 telocentric chromosomes. Analysis of active nucleolar organizer regions (NORs) by silver staining did not show any differences in number and chromosomal position in different populations. But FISH data showed significant difference between the populations, four of the five populations showed six 18S (three pairs) and two 5S (one pair) signals with positional polymorphism, while one population showed eight 18S and four 5S signals, respectively. Southern blot data confirms that 5S rDNA clusters present on two different chromosome pairs in Kosi river population contain non-transcribed spacers (NTS) of same length. In the present study, simultaneous localization of 45S and 5S rDNA by in situ hybridization helped us to develop the discrete population-specific markers in different geographically isolated populations of T. putitora.
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Affiliation(s)
- Mamta Singh
- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226 002, India
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21
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Singh M, Kumar R, Nagpure NS, Kushwaha B, Mani I, Lakra WS. Extensive NOR site polymorphism in geographically isolated populations of Golden mahseer, Tor putitora. Genome 2010; 52:783-9. [PMID: 19935926 DOI: 10.1139/g09-052] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Analyses of nucleolar organizer region (NOR) site polymorphism using silver staining were carried out in 72 individuals of 5 geographically isolated populations of Tor putitora from India. All Ag-NORs analyzed were constituted by rDNA that was confirmed by the presence of positive fluorescence in situ hybridization (FISH) signals. Analyses of the extra NORs among the populations confirmed the hypothesis that multi-chromosomal NOR site polymorphism is not an exception but a rule. We found a negative correlation between the mean number of extra NORs and geographical distance from the Alaknanda River population, and a significant positive correlation between the genetic distances obtained by NOR data and geographical distances among the isolated populations. These findings suggest a single geographical origin of this NOR polymorphism, from which it might have radiated to neighboring populations before their isolation. The distribution of NOR site variation was compared with the sequence variation of the ITS1 region of major rDNA (45S) and the two were found to be positively related. Different mechanisms such as transposable elements adjacent to ribosomal genes, repetitive elements which could serve as a point for chromosome exchange, amplification of minor rDNA loci, and reinsertion of extrachromosomal rDNA amplified during oogenesis have been proposed to explain the apparent NOR site polymorphism. The high dispersion of NOR site variants within and among the populations suggests that whatever transposition phenomenon is responsible for repetitive DNA or NOR jumping, it could still be active in T. putitora.
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Affiliation(s)
- Mamta Singh
- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow 226 002, U.P., India
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22
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Management units of brown trout from Galicia (NW: Spain) based on spatial genetic structure analysis. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9934-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Veltsos P, Keller I, Nichols RA. Geographically localised bursts of ribosomal DNA mobility in the grasshopper Podisma pedestris. Heredity (Edinb) 2009; 103:54-61. [PMID: 19384343 DOI: 10.1038/hdy.2009.32] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We report extraordinary variation in the number and the chromosomal location of ribosomal DNA (rDNA) arrays within populations of the alpine grasshopper Podisma pedestris; even greater differences were found between populations. The sites were detected by in situ hybridisation of labelled rDNA to chromosomal preparations. The total number of rDNA sites in an individual varied from three to thirteen. In the most extreme case, individuals from populations only 10 km apart had no rDNA loci in common. A survey of the geographical distribution of this variation identified clusters of populations with relatively similar chromosomal distribution of rDNA loci. These clusters correspond to those identified earlier by analysis of rDNA sequences. To explain this geographical clustering, we reconstructed the post-glacial colonisation of the region by assuming that the species' distribution has ascended to its current altitudinal range as the climate warmed. The reconstruction suggests that each cluster is descended from a colonisation route up a different alpine valley. That history would imply rapid establishment of rDNA differences, conceivably during the last 10,000 years since the last glaciation. The proposal for rapid change is consistent with the extensive within-population variation, which indicates that the processes responsible for the change in rDNA's chromosomal location continue to occur at a higher rate. We discuss whether our reconstruction of colonisation routes implies movement of the hybrid zone, which would indicate that a neo-XY sex chromosome system has spread through extant populations.
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Affiliation(s)
- P Veltsos
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK.
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24
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High Ag-NOR-site variation associated to a secondary contact in brown trout from the Iberian Peninsula. Genetica 2008; 136:419-27. [PMID: 19112557 DOI: 10.1007/s10709-008-9342-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Accepted: 12/06/2008] [Indexed: 10/21/2022]
Abstract
The analysis of nucleolar organizer regions (NORs) using silver (Ag-) staining and in situ hybridization (ISH) in brown trout (Salmo trutta) from various river basins in the Iberian Peninsula revealed high variation in the number and location of NORs. A total of 17 different Ag-NOR sites were revealed in 10 different chromosome pairs. Three different Ag-NOR patterns clustered by river basins and strongly associated to the internal transcribed spacer 1 (ITS1) variation were detected. The main variability in NOR-sites was found in a secondary contact between two divergent lineages of brown trouts at Duero basin. Our results confirmed the abrupt break in the spatial distribution of genetic variation of brown trout populations previously reported at Duero basin. We hypothesize that NOR-site variation might be a consequence of hybridization between divergent lineages of brown trouts and that NORs could play a major role in the maintenance of a hybrid zone in Duero basin via post-zygotic isolation mechanisms.
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25
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Cabrero J, Camacho JPM. Location and expression of ribosomal RNA genes in grasshoppers: abundance of silent and cryptic loci. Chromosome Res 2008; 16:595-607. [PMID: 18431681 DOI: 10.1007/s10577-008-1214-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2008] [Revised: 02/02/2008] [Accepted: 02/02/2008] [Indexed: 12/01/2022]
Abstract
We investigate regularities and restrictions in chromosome location of ribosomal RNA genes, analysed by fluorescent in situ hybridization (FISH), and their phenotypic expression assessed by nucleolus formation at first meiotic prophase cells, analysed by silver impregnation, in 49 grasshopper species. High variation was found for rDNA location between species within most genera analysed. The mean haploid number of rDNA loci detected by FISH was 2.47, but some species had up to 10 loci. Chromosome distribution of rDNA loci differed between the Gomphocerinae and Oedipodinae subfamilies, most loci being proximal to the centromere in the former and distal to it in the latter. Chromosomes 2, 3 and X frequently carried rDNA in Gomphocerinae species with 2n male symbol=17 chromosomes, whereas chromosomes 6 and 9 were the most frequent rDNA locations in the Oedipodinae. About 13% of the 126 rDNA loci detected by FISH were silent, although this figure might be even higher. The comparison of FISH and silver-impregnation results also suggested the existence of cryptic NORs, i.e. those forming small nucleoli with no apparent presence of rDNA revealed by FISH. This was especially clear after the same cells in two species were sequentially treated with both silver impregnation and FISH. The abundance of silent and cryptic loci might thus suggest that rDNA spreads through grasshopper genomes by the Dubcovsky and Dvorak mechanism-that is, the transposition of a few rRNA genes to new chromosome locations, their amplification giving rise to new NORs, and the elimination of the old NORs. The cryptic NORs might correspond to nascent NORs, i.e. a few rRNA gene copies moved to new locations, whereas the inactive rDNA loci might correspond to those being in the process of elimination.
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Affiliation(s)
- Josefa Cabrero
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain.
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26
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Bi K, Bogart JP, Fu J. Genealogical relationships of southern Ontario polyploid unisexual salamanders (genus Ambystoma) inferred from intergenomic exchanges and major rDNA cytotypes. Chromosome Res 2008; 16:275-89. [DOI: 10.1007/s10577-007-1192-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2007] [Revised: 11/28/2007] [Accepted: 11/28/2007] [Indexed: 11/30/2022]
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27
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Abdelaziz M, Teruel M, Chobanov D, Camacho JPM, Cabrero J. Physical mapping of rDNA and satDNA in A and B chromosomes of the grasshopper Eyprepocnemis plorans from a Greek population. Cytogenet Genome Res 2007; 119:143-6. [PMID: 18160794 DOI: 10.1159/000109631] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Accepted: 04/05/2007] [Indexed: 11/19/2022] Open
Abstract
Adult males and females of the grasshopper Eyprepocnemis plorans from a Greek population were analysed by C-banding, silver impregnation and double FISH for two DNA probes, i.e. ribosomal DNA (rDNA) and a 180-bp tandem repeat DNA (satDNA). This population shows characteristics of rDNA location in A chromosomes that are intermediate between those previously reported for eastern (Caucasus) and western (Spain and Morocco) populations. The four rDNA clusters revealed by FISH in chromosomes X, 9, 10 and 11 in Greek specimens imply two more than the two observed in chromosomes 9 and 11 in the Caucasus, but less than the 12 observed in all chromosomes in Morocco. Remarkably, the X chromosome bears one of the new rDNA locations in Greece with respect to the Caucasus, but it appears to be inactive, in contrast to X chromosomes in western populations, which are usually active. B chromosomes were very frequent in the Greek population, and three variants differing in size were observed, all of these being largely composed of rDNA, with the exception of a small pericentromeric satDNA cluster. The high B frequency suggests that B chromosomes in this population might behave parasitically, in resemblance to Bs in western populations.
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Affiliation(s)
- M Abdelaziz
- Departamento de Genética, Universidad de Granada, Spain
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28
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Gernand D, Golczyk H, Rutten T, Ilnicki T, Houben A, Joachimiak AJ. Tissue culture triggers chromosome alterations, amplification, and transposition of repeat sequences in Allium fistulosum. Genome 2007; 50:435-42. [PMID: 17612612 DOI: 10.1139/g07-023] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Structural alterations in nuclei and chromosomes of cells derived from callus culture of Allium fistulosum have been studied with fluorescent in situ hybridization (FISH) using 5S ribosomal DNA (rDNA), 45S rDNA, and 375-bp repeat probes. A high frequency of chromosome abnormalities was found to be caused by the loss of telomere-located 375-bp repeats, chromosome fusion, and subsequent breakage-fusion-bridge cycles. Products of chromosome fusions and monocentric and regularly shaped chromosomes showed additional 375-bp repeat and 45S rDNA clusters at unusual sites, suggesting dynamic copy-number changes and transposition of these repeats. Southern hybridization revealed no differences in the 375-bp repeat and 45S rDNA repeat array order or the degree of methylation between DNA isolated from leaves or tissue-culture cells. In addition, protruding, spike-like structures positive for 375-bp repeats were identified on the surface of different-sized nuclei. Transmission electron microscopy analysis revealed the accumulation of densely packed chromatin within spike-like structures. Because root calyptra cells showed similar structures, it is likely that heterochromatic spike-like structures are a feature of nondividing cells at the onset of programmed cell death.
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Affiliation(s)
- Dorota Gernand
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany
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29
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Mitochondrial haplotype variability of brown trout populations from Northwestern Iberian Peninsula, a secondary contact area between lineages. CONSERV GENET 2007. [DOI: 10.1007/s10592-007-9398-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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30
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Nieto Feliner G, Rosselló JA. Better the devil you know? Guidelines for insightful utilization of nrDNA ITS in species-level evolutionary studies in plants. Mol Phylogenet Evol 2007; 44:911-9. [PMID: 17383902 DOI: 10.1016/j.ympev.2007.01.013] [Citation(s) in RCA: 254] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Revised: 12/03/2006] [Accepted: 01/10/2007] [Indexed: 11/20/2022]
Abstract
The internal transcribed spacers (ITS) of the nuclear ribosomal 18S-5.8S-26S cistron continue to be the most popular non-plastid region for species-level phylogenetic studies of plant groups despite the early warnings about their potential flaws, which may ultimately result in incorrect assumptions of orthology. It has been gradually realized that the alternative target regions in the nuclear genome (low-copy nuclear genes, LCNG) are burdened with similar problems. The consequence is that, to date, developing useful LCNG for non-model organisms requires an investment in time and effort that hinders its use as a real practical alternative for many labs. It is here argued that ITS sequences, despite drawbacks, can still produce insightful results in species-level phylogenetic studies or when non-anonymous nuclear markers are required, provided that a thoughtful use of them is made. To facilitate this, two series of guidelines are proposed. One helps to circumvent problems of ITS amplification from the target organism, including spurious results from contaminants, paralogs and pseudogenes, as well as detection of sequencing artifacts. The other series helps to find out causes for unresolved clades in phylogenetic reconstruction, to integrate gene phylogenies, to distinguish horizontal transfer from lineage sorting, and to reveal if ITS phylogeny is not a good estimate of organism phylogeny.
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31
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Cabrero J, Perfectti F, Gómez R, Camacho JPM, López-León MD. Population variation in the A chromosome distribution of satellite DNA and ribosomal DNA in the grasshopper Eyprepocnemis plorans. Chromosome Res 2004; 11:375-81. [PMID: 12906134 DOI: 10.1023/a:1024127525756] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The double FISH analysis of two repetitive DNAs (a satellite DNA and ribosomal DNA) in 12 natural populations of the grasshopper Eyprepocnemis plorans collected at the south (Granada and Málaga provinces) and south-east (Albacete and Murcia provinces) of the Iberian Peninsula has shown their wide-spread presence throughout the whole genome as well as extensive variation among populations. Both DNAs are found in most A chromosomes. Regularly, both DNAs occurred in the S11 and X chromosomes, rDNA in the S10 and satDNA in the L2 and M3. No correlation was found between the number of satDNA and rDNA clusters in the A genomes of the 12 populations analysed, and both figures were independent of the presence of B chromosomes. The genomic distribution of both DNAs showed no association with the geographical localization of the populations analysed. Finally, we provide evidence that the supernumerary chromosome segment proximally located on the S11 chromosome is, in most cases, the result of satDNA amplification but, in some cases, it might also derive from amplification of both satDNA and rDNA.
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Affiliation(s)
- J Cabrero
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain.
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32
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Araújo SMSR, Silva CC, Pompolo SG, Perfectti F, Camacho JPM. Genetic load caused by variation in the amount of rDNA in a wasp. Chromosome Res 2003; 10:607-13. [PMID: 12498349 DOI: 10.1023/a:1020970820513] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Extensive variation in the size of the short (heterochromatic) arm of chromosome 14 was found in the wasp Trypoxylon (Trypargilum) albitarse. Ten different variants were differentiated by size and C-banding pattern. Fluorescent in-situ hybridization (FISH) revealed that ribosomal DNA in this species is clustered in the darkly C-banded parts of the heterochromatic short arm of chromosome 14. On this basis, we got an indirect estimate of the amount of rDNA from the area of these dark C-bands. The significant absence in males of the three chromosome variants with lower amounts of rDNA indicates that these three variants are lethal in this sex, and suggests the existence of a threshold marking the minimum amount of rDNA which is tolerable in haploidy. This implies about 4% genetic load in the population caused by variation in rDNA amount.
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Affiliation(s)
- S M S R Araújo
- Departamento de Biologia Celular, Universidade Estadual de Campinas , 13083 Campinas, SP, Brazil
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33
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Cabrero J, Bugrov A, Warchałowska-Sliwa E, López-León MD, Perfectti F, Camacho JPM. Comparative FISH analysis in five species of Eyprepocnemidine grasshoppers. Heredity (Edinb) 2003; 90:377-81. [PMID: 12714983 DOI: 10.1038/sj.hdy.6800255] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The chromosomal localization of ribosomal DNA, and a 180 bp satellite DNA isolated from Spanish Eyprepocnemis plorans specimens, has been analysed in five Eyprepocnemidinae species collected in Russia and Central Asia. Caucasian E. plorans individuals carried each of the two DNAs, but the rDNA was limited to only two chromosomes (S(9) and S(11)) in sharp contrast to Spanish specimens that show 4-8 rDNA clusters and to Moroccan specimens which carry rDNA in almost all chromosomes. The four remaining species, however, lacked the 180 bp tandem repeat, and showed rDNA clusters in one (S(9) in Thisoicetrinus pterostichus), two (S(9) and S(10) in Eyprepocnemis unicolor; M(8) and S(11) in Heteracris adspersa), or three (S(9), S(10), and S(11) in Shirakiacris shirakii) chromosome pairs. The implications of these findings for the evolution of these two chromosome markers in this group of species are discussed.
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Affiliation(s)
- J Cabrero
- Departamento de Genética, Universidad de Granada, 18071 Granada, Spain.
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Presa P, Pardo BG, Martínez P, Bernatchez L. Phylogeographic congruence between mtDNA and rDNA ITS markers in brown trout. Mol Biol Evol 2002; 19:2161-75. [PMID: 12446808 DOI: 10.1093/oxfordjournals.molbev.a004041] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Variation in the internal transcribed spacer (ITS) of rDNA was examined throughout the range of the brown trout (Salmo trutta) to analyze the usefulness of this molecular marker for phylogeographic analysis. The results were compared with those previously obtained with mtDNA, a region exhaustively analyzed along the brown trout distribution. ITS2 was essentially conserved at all populations sampled, no informative characters being detected across the main lineages described in this species. Conversely, ITS1 showed a greater homogenization than other genetic markers at a microgeographic scale, with variation partitioning into several major phylogenetic groups. Phylogeographic patterns were partially congruent between both ITS1 and mtDNA. The main discrepancies were the detection of intra-individual variation and putative recombinant ITS1 sequences in hybridization areas between genetically different, yet historically overlapping, assemblages. Also, the existence of an ancient ITS1 sequence in the Mediterranean-southeastern area (rMEDA), not revealed by mtDNA analysis, was evidenced after rDNA ITS1 analysis.
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Affiliation(s)
- P Presa
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, Spain
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Jankun M, Martinez P, Pardo BG, Kirtiklis L, Rab P, Rabova M, Sanchez L. Ribosomal genes in Coregonid fishes (Coregonus lavaretus, C. albula and C. peled) (Salmonidae): single and multiple nucleolus organizer regions. Heredity (Edinb) 2001; 87:672-9. [PMID: 11903562 DOI: 10.1046/j.1365-2540.2001.00964.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Major rDNA loci, i.e. nucleolus-organizing regions (NORs), were assigned using chromomycin-A3 (CMA3) staining followed by sequential silver (Ag) staining and in situ hybridization (ISH) with a rDNA probe to the chromosomes of the European whitefish (Coregonus lavaretus), the peled (Coregonus peled) and the vendace (Coregonus albula), three closely related coregonine salmonid fishes. One pair of NOR-bearing chromosomes was found in the peled karyotype. Multichromosomal, but stable, locations of rDNA sites on three pairs of chromosomes were observed in the European whitefish karyotype. Multichromosomal polymorphic locations, both in site and number, were observed in the karyotype of the vendace. Several Ag-, CMA3- and ISH-positive regions were found which defined up to seven cytotypes of five NOR-bearing chromosomes. All positive Ag-NORs detected corresponded both to rDNA-ISH- and CMA3-positive signals, which suggests extensive structural polymorphism in the locations of rDNA sites. Stable NOR sites were found at the same location on both homologous elements of the chromosome no. 9 in all individuals, while the remaining NORs were quite variable between individuals, and often present in heterozygous condition. The apparently similar and parallel evolutionary rDNA differentiation patterns in the subfamilies Coregoninae and Salmoninae (family Salmonidae) are observed and discussed.
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Affiliation(s)
- M Jankun
- University WM in Olsztyn, Department of Evolutionary Ecology, 10-718 Olsztyn-Kortowo, Poland.
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Bouza C, Castro J, Sánchez L, Martínez P. Allozymic evidence of parapatric differentiation of brown trout (Salmo trutta L.) within an Atlantic river basin of the Iberian Peninsula. Mol Ecol 2001; 10:1455-69. [PMID: 11412368 DOI: 10.1046/j.1365-294x.2001.01272.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The genetic variation of brown trout from Duero, one of the main Atlantic Iberian river basins, was assessed at 34 enzymatic loci in 62 native populations. A strong intrabasin differentiation was detected (G(ST) = 0.46; range D: 0-0.066), mainly attributable to the existence of two divergent groups of populations within Duero: southern and northern groups. This divergence was mainly a consequence of the unequal distribution of *75 and *100 alleles at sMDH-B1,2* isoloci, which were correlated with substantial differences in genetic diversity among regions. The Lower Course region (nearly fixed for the *100 allele) and Pisuerga River (nearly fixed for the *75 allele) showed lower heterozygosities (H approximately 0.8%) in contrast with adjacent areas, which evidenced intermediate frequencies for both alleles and higher heterozygosities (H: 2.2-3.1%). Vicariance appeared as the more probable explanation for the significant positive correlation detected between genetic and geographical distances in Duero Basin. Genetic relationships with adjacent Iberian drainages indicate a close similarity between the southern group and Cantabric trout, whereas the northern group constitutes an ancient form from this basin. This study confirmed complex genetic relationships in brown trout from northwest Iberia, reasserting the existence of clines at several loci and for genetic diversity. The interaction between Cantabric and Duero trout, as well as the location of the limit of the anadromous form around the 42 degrees N parallel, are both required to understand the genetic characteristics of brown trout from this area.
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Affiliation(s)
- C Bouza
- Departamento de Biología Fundamental, Area de Genética, Universidad de Santiago de Compostela, Facultad de Veterinaria, 27002 Lugo, Spain
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