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Tavares MG, Teixeira GA. Cytogenetic characterization of solitary wasp Ancistrocerus flavomarginatus (Brèthes, 1906) (Hymenoptera, Vespidae) with insights into the chromosomal evolution in the genus. Genome 2023; 66:62-67. [PMID: 36645884 DOI: 10.1139/gen-2022-0095] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Cytogenetic studies have enabled the characterization of the chromosomal macrostructure and microstructure and have contributed to the understanding of the evolution of wasp karyotypes. However, studies on Eumeninae solitary wasps are scarce. In this study, we characterized the karyotype of Ancistrocerus flavomarginatus (Brèthes, 1906) and compared it with previous data from other Ancistrocerus (Wesmael, 1836) species to shed light on the chromosomal diversity of the genus. A chromosome number of 2n = 24 in females and n = 12 in males was observed. Comparing the A. flavomarginatus karyotype with that of another Ancistrocerus species showed variations in the morphology of some chromosomal pairs. The presence of two larger chromosome pairs, almost entirely heterochromatic, and the predominance of subtelocentric chromosomes with heterochromatic short arms in A. flavomarginatus support the occurrence of fissions in Ancistrocerus. A single site of ribosomal genes was observed in A. flavomarginatus, in addition to a size polymorphism of these rDNA clusters between the homologues of some analyzed females. This polymorphism may originate from duplications/deletions due to unequal crossing-over or amplification via transposable elements. The (GA)15 microsatellite is located exclusively in euchromatic regions. Our data show that different rearrangements seem to shape chromosomal evolution in Ancistrocerus species.
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Affiliation(s)
- Mara Garcia Tavares
- Laboratory of Insect Cytogenetics, Department of General Biology, CCB, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Gisele Amaro Teixeira
- Laboratory of Insect Cytogenetics, Department of General Biology, CCB, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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2
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Silva GS, Souza MM, Carvalho Cayres Pamponét V. Identification of 45S rDNA in Passiflora using low coverage sequencing: analysis of GC content and chromosomal localization. Mol Biol Rep 2022; 49:8555-8566. [PMID: 35997851 DOI: 10.1007/s11033-022-07686-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 06/08/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND The 45S rDNA is considered the most useful chromosomal marker for cytogenetic analysis of Passiflora. Amplification of 45S rDNA sequence via PCR are more advantageous than sequence maintenance in vectors for chromosomal hybridization via FISH. We aimed both to identify 45S rDNA by sequencing data for chromosomal localization and to verify the relationship between GC content and CMA3/DAPI banding. METHODS AND RESULTS Low-coverage sequencing of Passiflora alata, P. cincinnata, and P. edulis was performed, and 45S rDNA units were identified using RepeatExplorer. The 45S rDNA units were used to construct a neighbor-joining tree to verify the similarities between the three species' 18S and 26S rDNA sequences. Clusters (CL)116 (P. alata), CL71 (P. cincinnata), and CL116 (P. edulis) were remarkably similar among the three species, and the 26S rDNA sequences of the clusters were similar to those of Populus tremuloides, Salix interior, and Averrhoa carambola (98% identity). The 26S rDNA was cytologically localized in the chromosomes of P. edulis, P. bahiensis, and the backcrossed hybrid (P. sublanceolata vs. HD13). The hybridization transfer capacity was evaluated in Citrus sunki and Cucumis melo. Finally, a chromosomal pair with a heteromorphic 26S rDNA site was observed in P. edulis, which was the same to that observed for CMA3. CONCLUSION The amplification of the 26S rDNA in Passiflora via PCR and the chromosomal localization in Passiflora and other plant species was successfully achieved. The CMA3 bands were found to be related not only to the amount of GC but also to its structure and the number of repetitions.
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Affiliation(s)
- Gonçalo Santos Silva
- Laboratório de Melhoramento de Plantas (LAMEP), Departamento de Ciências Biológicas (DCB), Universidade Estadual de Santa Cruz (UESC), Rod. Jorge Amado, Km 16, Salobrinho, Ilhéus, BA, 45662-900, Brasil
| | - Margarete Magalhães Souza
- Laboratório de Melhoramento de Plantas (LAMEP), Departamento de Ciências Biológicas (DCB), Universidade Estadual de Santa Cruz (UESC), Rod. Jorge Amado, Km 16, Salobrinho, Ilhéus, BA, 45662-900, Brasil.
| | - Vanessa Carvalho Cayres Pamponét
- Laboratório de Melhoramento de Plantas (LAMEP), Departamento de Ciências Biológicas (DCB), Universidade Estadual de Santa Cruz (UESC), Rod. Jorge Amado, Km 16, Salobrinho, Ilhéus, BA, 45662-900, Brasil
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3
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Alexandrov OS, Romanov DV, Divashuk MG, Razumova OV, Ulyanov DS, Karlov GI. Study and Physical Mapping of the Species-Specific Tandem Repeat CS-237 Linked with 45S Ribosomal DNA Intergenic Spacer in Cannabis sativa L. PLANTS (BASEL, SWITZERLAND) 2022; 11:1396. [PMID: 35684169 PMCID: PMC9183113 DOI: 10.3390/plants11111396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/11/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Hemp (Cannabis sativa L.) is a valuable crop and model plant for studying sex chromosomes. The scientific interest in the plant has led to its whole genome sequencing and the determination of its cytogenetic characteristics. A range of cytogenetic markers (subtelomeric repeat CS-1, 5S rDNA, and 45S rDNA) has been mapped onto hemp's chromosomes by fluorescent in situ hybridization (FISH). In this study, another cytogenetic marker (the tandem repeat CS-237, with a 237 bp monomer) was found, studied, and localized on chromosomes by FISH. The signal distribution and karyotyping revealed that the CS-237 probe was localized in chromosome 6 with one hybridization site and in chromosome 8 with two hybridization sites, one of which colocalizes with the 45S rDNA probe (with which a nucleolus organizer region, NOR, was detected). A BLAST analysis of the genomic data and PCR experiments showed that the modified CS-237 monomers (delCS-237, 208 bp in size) were present in the intergenic spacers (IGSs) of hemp 45S rDNA monomers. Such a feature was firstly observed in Cannabaceae species. However, IGS-linked DNA repeats were found in several plant species of other families (Fabaceae, Solanaceae, and Asteraceae). This phenomenon is discussed in this article. The example of CS-237 may be useful for further studying the phenomenon as well as for the physical mapping of hemp chromosomes.
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Affiliation(s)
| | - Dmitry V. Romanov
- All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya 42, 127550 Moscow, Russia; (O.S.A.); (M.G.D.); (O.V.R.); (D.S.U.); (G.I.K.)
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Rosselló JA, Maravilla AJ, Rosato M. The Nuclear 35S rDNA World in Plant Systematics and Evolution: A Primer of Cautions and Common Misconceptions in Cytogenetic Studies. FRONTIERS IN PLANT SCIENCE 2022; 13:788911. [PMID: 35283933 PMCID: PMC8908318 DOI: 10.3389/fpls.2022.788911] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 01/27/2022] [Indexed: 05/04/2023]
Abstract
The ubiquitous presence of rRNA genes in nuclear, plastid, and mitochondrial genomes has provided an opportunity to use genomic markers to infer patterns of molecular and organismic evolution as well as to assess systematic issues throughout the tree of life. The number, size, location, and activity of the 35S rDNA cistrons in plant karyotypes have been used as conventional cytogenetic landmarks. Their scrutiny has been useful to infer patterns of chromosomal evolution and the data have been used as a proxy for assessing species discrimination, population differentiation and evolutionary relationships. The correct interpretation of rDNA markers in plant taxonomy and evolution is not free of drawbacks given the complexities derived from the lability of the genetic architecture, the diverse patterns of molecular change, and the fate and evolutionary dynamics of the rDNA units in hybrids and polyploid species. In addition, the terminology used by independent authors is somewhat vague, which often complicates comparisons. To date, no efforts have been reported addressing the potential problems and limitations involved in generating, utilizing, and interpreting the data from the 35S rDNA in cytogenetics. This review discusses the main technical and conceptual limitations of these rDNA markers obtained by cytological and karyological experimental work, in order to clarify biological and evolutionary inferences postulated in a systematic and phylogenetic context. Also, we provide clarification for some ambiguity and misconceptions in terminology usually found in published work that may help to improve the usage of the 35S ribosomal world in plant evolution.
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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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Ali HBM, Osman SA. Genetic relationship study of some Vicia species by FISH and total seed storage protein patterns. J Genet Eng Biotechnol 2020; 18:37. [PMID: 32737692 PMCID: PMC7394970 DOI: 10.1186/s43141-020-00054-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/16/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND Genus Vicia is a member of family Fabaceae and comprises 180 to 210 species. The most important species is faba bean (Vicia faba) which is still one of the most favourable grain legumes over all the world. The genus contains some additional food crops and a number of forage plants and some other weedy strains such as Vicia angustifolia and Vicia cordata. The aim of the present investigation is to elucidate the phylogenetic relationships among four Vicia species, two species (Vicia angustifolia L. ssp. Angustifolia (2n = 12) and Vicia cordata wulfen ex Hoppe (2n = 10)) belong to section Vicia, Vicia dalmatica A. Kern (2n = 12, section Cracca), and Vicia johannis tamamsch (2n = 14, section Faba). RESULTS Two tools have been applied to identify the genetic relationships among the examined species, double fluorescence in situ hybridization (FISH) has been used to localize the sites of 5S and 45S rDNA, and sodium dodecyl sulfate-poly acrylamide gel electrophoretic (SDS-PAGE) patterns of total seed storage protein fractions. Double FISH experiment has not shown any variation in the loci number, but the positions along the chromosomes were different; both Vicia johannis and Vicia dalmatica exhibited the same interstitial 45S rRNA gene loci, while Vicia angustifolia and Vicia cordata have shown single large stretched 45S rRNA loci almost at the terminal region of the shortest chromosome. It could be concluded from the similarity matrix among the Vicia species as computed according to Jaccard coefficient from the SDS-PAGE, that V. cordata is similar to V. angustifolia and V. dalmatica by a percentage of 73 and 69%, respectively, and the most related species to V. johannis is V. dalmatica (~ 64%). CONCLUSION FISH and SDS-PAGE of the total seed storage proteins together reflected the similar genetic relationship among the studied species as fellows, V. angustifolia is more related to V. cordata then comes V. dalmatica and then V. johannis which is at a distal position from the other species.
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Affiliation(s)
- Hoda B M Ali
- Genetics and Cytology Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, P.O, Giza, 12622, Egypt.
| | - Samira A Osman
- Genetics and Cytology Department, Genetic Engineering and Biotechnology Research Division, National Research Centre, P.O, Giza, 12622, Egypt
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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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8
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Ávila Robledillo L, Koblížková A, Novák P, Böttinger K, Vrbová I, Neumann P, Schubert I, Macas J. Satellite DNA in Vicia faba is characterized by remarkable diversity in its sequence composition, association with centromeres, and replication timing. Sci Rep 2018; 8:5838. [PMID: 29643436 PMCID: PMC5895790 DOI: 10.1038/s41598-018-24196-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/28/2018] [Indexed: 11/17/2022] Open
Abstract
Satellite DNA, a class of repetitive sequences forming long arrays of tandemly repeated units, represents substantial portions of many plant genomes yet remains poorly characterized due to various methodological obstacles. Here we show that the genome of the field bean (Vicia faba, 2n = 12), a long-established model for cytogenetic studies in plants, contains a diverse set of satellite repeats, most of which remained concealed until their present investigation. Using next-generation sequencing combined with novel bioinformatics tools, we reconstructed consensus sequences of 23 novel satellite repeats representing 0.008–2.700% of the genome and mapped their distribution on chromosomes. We found that in addition to typical satellites with monomers hundreds of nucleotides long, V. faba contains a large number of satellite repeats with unusually long monomers (687–2033 bp), which are predominantly localized in pericentromeric regions. Using chromatin immunoprecipitation with CenH3 antibody, we revealed an extraordinary diversity of centromeric satellites, consisting of seven repeats with chromosome-specific distribution. We also found that in spite of their different nucleotide sequences, all centromeric repeats are replicated during mid-S phase, while most other satellites are replicated in the first part of late S phase, followed by a single family of FokI repeats representing the latest replicating chromatin.
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Affiliation(s)
- Laura Ávila Robledillo
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic.,University of South Bohemia, Faculty of Science, České Budějovice, 37005, Czech Republic
| | - Andrea Koblížková
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic
| | - Petr Novák
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic
| | - Katharina Böttinger
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic.,University of South Bohemia, Faculty of Science, České Budějovice, 37005, Czech Republic
| | - Iva Vrbová
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic
| | - Pavel Neumann
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466, Gatersleben, Stadt Seeland, Germany
| | - Jiří Macas
- Biology Centre of the Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, 37005, Czech Republic.
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9
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Novák P, Ávila Robledillo L, Koblížková A, Vrbová I, Neumann P, Macas J. TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res 2017. [PMID: 28402514 DOI: 10.1093/nar/gkx257.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads. The pipeline first employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. Putative satellite repeats are subsequently detected by the presence of circular structures in their cluster graphs. Consensus sequences of repeat monomers are then reconstructed from the most frequent k-mers obtained by decomposing read sequences from corresponding clusters. The pipeline performance was successfully validated by analyzing low-pass genome sequencing data from five plant species where satellite DNA was previously experimentally characterized. Moreover, novel satellite repeats were predicted for the genome of Vicia faba and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence in situ hybridization.
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Affiliation(s)
- Petr Novák
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Laura Ávila Robledillo
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Andrea Koblížková
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Iva Vrbová
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Pavel Neumann
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Jirí Macas
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
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10
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Novák P, Ávila Robledillo L, Koblížková A, Vrbová I, Neumann P, Macas J. TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res 2017; 45:e111. [PMID: 28402514 PMCID: PMC5499541 DOI: 10.1093/nar/gkx257] [Citation(s) in RCA: 182] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/23/2017] [Accepted: 04/04/2017] [Indexed: 12/21/2022] Open
Abstract
Satellite DNA is one of the major classes of repetitive DNA, characterized by tandemly arranged repeat copies that form contiguous arrays up to megabases in length. This type of genomic organization makes satellite DNA difficult to assemble, which hampers characterization of satellite sequences by computational analysis of genomic contigs. Here, we present tandem repeat analyzer (TAREAN), a novel computational pipeline that circumvents this problem by detecting satellite repeats directly from unassembled short reads. The pipeline first employs graph-based sequence clustering to identify groups of reads that represent repetitive elements. Putative satellite repeats are subsequently detected by the presence of circular structures in their cluster graphs. Consensus sequences of repeat monomers are then reconstructed from the most frequent k-mers obtained by decomposing read sequences from corresponding clusters. The pipeline performance was successfully validated by analyzing low-pass genome sequencing data from five plant species where satellite DNA was previously experimentally characterized. Moreover, novel satellite repeats were predicted for the genome of Vicia faba and three of these repeats were verified by detecting their sequences on metaphase chromosomes using fluorescence in situ hybridization.
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Affiliation(s)
- Petr Novák
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Laura Ávila Robledillo
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Andrea Koblížková
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Iva Vrbová
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Pavel Neumann
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
| | - Jirí Macas
- Institute of Plant Molecular Biology, Biology Centre CAS, Ceské Budejovice CZ-37005, Czech Republic
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Rubert M, da Rosa R, Zawadzki CH, Mariotto S, Moreira-Filho O, Giuliano-Caetano L. Chromosome Mapping of 18S Ribosomal RNA Genes in Eleven Hypostomus Species (Siluriformes, Loricariidae): Diversity Analysis of the Sites. Zebrafish 2016; 13:360-8. [PMID: 27192329 DOI: 10.1089/zeb.2016.1279] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We investigated the chromosomal distribution of 18S ribosomal DNA (rDNA) in different populations of 11 species of Hypostomus collected in important Brazilian basins, namely South Atlantic, Upper Paraná, and Paraguay applying the fluorescence in situ hybridization (FISH). Hypostomus cochliodon, Hypostomus commersoni, Hypostomus hermanni, Hypostomus regani, Hypostomus albopunctatus, Hypostomus paulinus, Hypostomus aff. paulinus, Hypostomus iheringii, and Hypostomus mutucae presented multiple 18S rDNA sites while Hypostomus strigaticeps and Hypostomus nigromaculatus exhibited a single pair of chromosomes with 18S rDNA sites. The studied species presented variations in the number and position of these sites. The results accomplished were similar to those obtained by the analysis of AgNORs, revealing the same interspecific variability. Each species exhibited distinctive patterns of AgNOR and 18S rDNA distribution, which can be considered cytogenetic markers in each species of the genus and help improve the discussions on the phylogeny of the group.
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Affiliation(s)
- Marceléia Rubert
- 1 Laboratório de Biodiversidade Molecular e Conservação, Universidade Federal de São Carlos , São Carlos, Brazil
| | - Renata da Rosa
- 2 Laboratório de Citogenética Animal, Universidade Estadual de Londrina , Londrina, Brazil
| | - Claudio H Zawadzki
- 3 Núcleo de Pesquisas em Limnologia, Ictiologia e Aquicultura, Universidade Estadual de Maringá , Maringá, Brazil
| | - Sandra Mariotto
- 4 Instituto Federal de Educação Ciência e Tecnologia de Mato Grosso (IFMT) , Cuiabá, Brazil
| | - Orlando Moreira-Filho
- 1 Laboratório de Biodiversidade Molecular e Conservação, Universidade Federal de São Carlos , São Carlos, Brazil
| | - Lucia Giuliano-Caetano
- 2 Laboratório de Citogenética Animal, Universidade Estadual de Londrina , Londrina, Brazil
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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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Almeida C, Fonsêca A, dos Santos KGB, Mosiolek M, Pedrosa-Harand A. Contrasting evolution of a satellite DNA and its ancestral IGS rDNA in Phaseolus (Fabaceae). Genome 2012; 55:683-9. [PMID: 23050694 DOI: 10.1139/g2012-059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
CC4 is a satellite DNA from common bean (Phaseolus vulgaris L.) that is similar to its intergenic spacer (IGS) rDNA. CC4 was originally hypothesized to be an old, fast evolving satellite family that has invaded common bean rDNA. To test this hypothesis and contribute to the understanding of IGS-like satellite DNA evolution, we have investigated its distribution in the genus Phaseolus and related species. CC4 was cloned and used as probe for Southern blot and FISH experiments. CC4 was observed as an independent satellite in common bean, forming two to three major and a few minor pericentromeric clusters. In Phaseolus coccineus, CC4 was present in four major clusters, also not co-localized with the 45S rDNA sites. Remarkably, in the less related species of the genus, signals were detected co-localized with the 45S rDNA sites, but co-localization was not observed in the species where CC4 is present as an independent satellite. No signal was detected in species from related genera. Altogether, the data suggest that CC4 has originated from the IGS rDNA in the P. vulgaris-P. coccineus lineage and has evolved slower than the IGS rDNA from this lineage.
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Affiliation(s)
- Cícero Almeida
- Laboratory of Plant Cytogenetics and Molecular Biology, Department of Botany, Federal University of Pernambuco, Recife, PE, Brazil, 50670-420
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14
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Castro J, Sánchez L, Martínez P, Lucchini SD, Nardi I. Molecular analysis of a NOR site polymorphism in brown trout (Salmo trutta): organization of rDNA intergenic spacers. Genome 2012; 40:916-22. [PMID: 18464877 DOI: 10.1139/g97-118] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Using restriction endonuclease mapping, we have analyzed the organization of rDNA (DNA coding for ribosomal RNA (rRNA)) units in the salmonid fish Salmo trutta, as an initial step toward understand the molecular basis of a nucleolar organizer region (NOR) site polymorphism detected in this species. The size of the rDNA units ranged between 15 and 23 kb, with remarkable variation both within individuals and between populations. Three regions of internal tandem repetitiveness responsible for this length polymorphism were located to the intergenic spacers. NOR site polymorphic individuals showed a higher number of length classes, in some cases forming a complete 1 kb fragment ladder. The amount of rRNA genes was as much as 8-fold higher in polymorphic individuals compared with standard individuals. All individuals from the most polymorphic population showed a 14-kb insertion of unknown nature in a small proportion (below 25%) of the 28S rRNA genes.
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15
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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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Evolutionary dynamics of rDNA clusters on chromosomes of moths and butterflies (Lepidoptera). Genetica 2009; 138:343-354. [PMID: 19921441 DOI: 10.1007/s10709-009-9424-5] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Accepted: 11/03/2009] [Indexed: 01/05/2023]
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Jo SH, Koo DH, Kim JF, Hur CG, Lee S, Yang TJ, Kwon SY, Choi D. Evolution of ribosomal DNA-derived satellite repeat in tomato genome. BMC PLANT BIOLOGY 2009; 9:42. [PMID: 19351415 PMCID: PMC2679016 DOI: 10.1186/1471-2229-9-42] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Accepted: 04/08/2009] [Indexed: 05/03/2023]
Abstract
BACKGROUND Tandemly repeated DNA, also called as satellite DNA, is a common feature of eukaryotic genomes. Satellite repeats can expand and contract dramatically, which may cause genome size variation among genetically-related species. However, the origin and expansion mechanism are not clear yet and needed to be elucidated. RESULTS FISH analysis revealed that the satellite repeat showing homology with intergenic spacer (IGS) of rDNA present in the tomato genome. By comparing the sequences representing distinct stages in the divergence of rDNA repeat with those of canonical rDNA arrays, the molecular mechanism of the evolution of satellite repeat is described. Comprehensive sequence analysis and phylogenetic analysis demonstrated that a long terminal repeat retrotransposon was interrupted into each copy of the 18S rDNA and polymerized by recombination rather than transposition via an RNA intermediate. The repeat was expanded through doubling the number of IGS into the 25S rRNA gene, and also greatly increasing the copy number of type I subrepeat in the IGS of 25-18S rDNA by segmental duplication. Homogenization to a single type of subrepeat in the satellite repeat was achieved as the result of amplifying copy number of the type I subrepeat but eliminating neighboring sequences including the type II subrepeat and rRNA coding sequence from the array. FISH analysis revealed that the satellite repeats are commonly present in closely-related Solanum species, but vary in their distribution and abundance among species. CONCLUSION These results represent that the dynamic satellite repeats were originated from intergenic spacer of rDNA unit in the tomato genome. This result could serve as an example towards understanding the initiation and the expansion of the satellite repeats in complex eukaryotic genome.
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MESH Headings
- DNA, Plant/genetics
- DNA, Ribosomal Spacer/genetics
- DNA, Satellite/genetics
- Evolution, Molecular
- Genome, Plant
- In Situ Hybridization, Fluorescence
- Solanum lycopersicum/genetics
- Phylogeny
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 18S/genetics
- Retroelements
- Sequence Analysis, DNA
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Affiliation(s)
- Sung-Hwan Jo
- Plant Genome Research Center, KRIBB, Daejeon, 305-806, Korea
- Department of Functional Genomics, University of Science & Technology, Daejeon 305-333, Korea
- Omics and Integration Research Center, KRIBB, Daejeon, 305-806, Korea
| | - Dal-Hoe Koo
- Plant Genome Research Center, KRIBB, Daejeon, 305-806, Korea
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jihyun F Kim
- Systems Microbiology Research Center, KRIBB, Daejeon, 305-806, Korea
- Department of Functional Genomics, University of Science & Technology, Daejeon 305-333, Korea
| | - Cheol-Goo Hur
- Plant Genome Research Center, KRIBB, Daejeon, 305-806, Korea
- Omics and Integration Research Center, KRIBB, Daejeon, 305-806, Korea
| | - Sanghyeob Lee
- Plant Genome Research Center, KRIBB, Daejeon, 305-806, Korea
- Dongbu Advanced Research Institute, Dongbu HiTek Co, Ltd Daejeon 305-708, Korea
| | - Tae-jin Yang
- Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-742, Korea
| | - Suk-Yoon Kwon
- Plant Genome Research Center, KRIBB, Daejeon, 305-806, Korea
| | - Doil Choi
- Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-742, Korea
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18
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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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19
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Sarri V, Minelli S, Panara F, Morgante M, Jurman I, Zuccolo A, Cionini PG. Characterization and chromosomal organization of satellite DNA sequences in Picea abies. Genome 2008; 51:705-13. [PMID: 18772948 DOI: 10.1139/g08-048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Three clones containing satellite DNA sequences were selected from a randomly sheared genomic DNA library of Picea abies (clones PAF1, PAG004P22F (2F), and PAG004E03C (3C)). PAF1 contained 7 repeats that were 37-55 bp in length and had 68.9%-91.9% nucleotide sequence similarity. Two 2F repeats were 305-306 bp in length and had 83% sequence similarity. Two 3C repeats were 193-226 bp in length and had a sequence similarity of 78.6%. The copy number per 1C DNA of PAF1, 2F, and 3C repeats was 2.7 x 10(6), 2.9 x 10(5), and 2.9 x 10(4), respectively. In situ hybridization showed centromeric localization of these sequences in two chromosome pairs with PAF1, all pairs but one with 2F, and three pairs with 3C. Moreover, PAF1 sequences hybridized at secondary constrictions in six pairs, while 2F-related sequences were found at these chromosome regions only in four pairs. These hybridization patterns allow all chromosome pairs to be distinguished. PAF1-related repeats were contained in the intergenic spacer (IGS) of ribosomal cistrons in all six nucleolar organizers of the complement, while sequences related to 2F were found on only one side of the rDNA arrays in four pairs, showing structural diversity between rDNA regions of different chromosomes.
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Affiliation(s)
- V Sarri
- Dipartimento di Biologia Cellulare e Ambientale, Sezione di Biologia Cellulare e Molecolare, Universita di Perugia, Via Elce di Sotto, 06123 Perugia, Italy
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20
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Guggisberg A, Baroux C, Grossniklaus U, Conti E. Genomic origin and organization of the allopolyploid Primula egaliksensis investigated by in situ hybridization. ANNALS OF BOTANY 2008; 101:919-27. [PMID: 18308718 PMCID: PMC2710232 DOI: 10.1093/aob/mcn026] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2007] [Revised: 12/20/2007] [Accepted: 02/04/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Earlier studies have suggested that the tetraploid Primula egaliksensis (2n = 40) originated from hybridization between the diploids P. mistassinica (2n = 18) and P. nutans (2n = 22), which were hypothesized to be the maternal and paternal parent, respectively. The present paper is aimed at verifying the hybrid nature of P. egaliksensis using cytogenetic tools, and to investigate the extent to which the parental genomes have undergone genomic reorganization. METHODS Genomic in situ hybridization (GISH) and fluorescent in situ hybridization (FISH) with ribosomal DNA (rDNA) probes, together with sequencing of the internal transcribed spacer (ITS) region of the rDNA, were used to identify the origin of P. egaliksensis and to explore its genomic organization, particularly at rDNA loci. KEY RESULTS GISH showed that P. egaliksensis inherited all chromosomes from P. mistassinica and P. nutans and did not reveal major intergenomic rearrangements between the parental genomes (e.g. interchromosomal translocations). However, karyological comparisons and FISH experiments suggested small-scale rearrangements, particularly at rDNA sites. Primula egaliksensis lacked the ITS-bearing heterochromatic knobs characteristic of the maternal parent P. mistassinica and maintained only the rDNA loci of P. nutans. These results corroborated sequence data indicating that most ITS sequences of P. egaliksensis were of the paternal repeat type. CONCLUSIONS The lack of major rearrangements may be a consequence of the considerable genetic divergence between the putative parents, while the rapid elimination of the ITS repeats from the maternal progenitor may be explained by the subterminal location of ITS loci or a potential role of nucleolar dominance in chromosome stabilization. These small-scale rearrangements may be indicative of genome diploidization, but further investigations are needed to confirm this assumption.
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Affiliation(s)
- Alessia Guggisberg
- Institut für Systematische Botanik & Zürich-Basel Plant Science Center, Universität Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland.
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21
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Abstract
Chromosomal data have been underutilized in phylogenetic investigations despite the obvious potential that cytogenetic studies have to reveal both structural and functional homologies among taxa. In large part this is associated with difficulties in scoring conventional and molecular cytogenetic information for phylogenetic analysis. The manner in which chromosomal data have been used by most authors in the past was often conceptionally flawed in terms of the methods and principles underpinning modern cladistics. We present herein a review of the different methods employed, examine their relative strengths, and then outline a simple approach that considers the chromosomal change as the character, and its presence or absence the character state. We test this using one simulated and several empirical data sets. Features that are unique to cytogenetic investigations, including B-chromosomes, heterochromatic additions/deletions, and the location and number of nucleolar organizer regions (NORs), as well as the weighting of chromosomal characters, are critically discussed with regard to their suitability for phylogenetic reconstruction. We conclude that each of these classes of data have inherent problems that limit their usefulness in phylogenetic analyses and in most of these instances, inclusion should be subject to rigorous appraisal that addresses the criterion of unequivocal homology.
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Affiliation(s)
- Gauthier Dobigny
- Museum National d'Histoire Naturelle, Laboratoire Origine, Structure et Evolution de la Biodiversité, 55, rue Buffon, F75005 Paris, France.
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22
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Lim KY, Skalicka K, Koukalova B, Volkov RA, Matyasek R, Hemleben V, Leitch AR, Kovarik A. Dynamic changes in the distribution of a satellite homologous to intergenic 26-18S rDNA spacer in the evolution of Nicotiana. Genetics 2004; 166:1935-46. [PMID: 15126410 PMCID: PMC1470824 DOI: 10.1534/genetics.166.4.1935] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An approximately 135-bp sequence called the A1/A2 repeat was isolated from the transcribed region of the 26-18S rDNA intergenic spacer (IGS) of Nicotiana tomentosiformis. Fluorescence in situ hybridization (FISH) and Southern blot analysis revealed its occurrence as an independent satellite (termed an A1/A2 satellite) outside of rDNA loci in species of Nicotiana section Tomentosae. The chromosomal location, patterns of genomic dispersion, and copy numbers of its tandemly arranged units varied between the species. In more distantly related Nicotiana species the A1/A2 repeats were found only at the nucleolar organizer regions (NOR). There was a trend toward the elimination of the A1/A2 satellite in N. tabacum (tobacco), an allotetraploid with parents closely related to the diploids N. sylvestris and N. tomentosiformis. This process may have already commenced in an S(3) generation of synthetic tobacco. Cytosine residues in the IGS were significantly hypomethylated compared with the A1/A2 satellite. There was no clear separation between the IGS and satellite fractions in sequence analysis of individual clones and we found no evidence for CG suppression. Taken together the data indicate a dynamic nature of the A1/A2 repeats in Nicotiana genomes, with evidence for recurrent integration, copy number expansions, and contractions.
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Affiliation(s)
- K Y Lim
- Institute of Biophysics, AV CR, 612 65 Brno, Czech Republic
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23
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Lim KY, Skalicka K, Koukalova B, Volkov RA, Matyasek R, Hemleben V, Leitch AR, Kovarik A. Dynamic Changes in the Distribution of a Satellite Homologous to Intergenic 26-18S rDNA Spacer in the Evolution of Nicotiana. Genetics 2004. [DOI: 10.1093/genetics/166.4.1935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
An ∼135-bp sequence called the A1/A2 repeat was isolated from the transcribed region of the 26-18S rDNA intergenic spacer (IGS) of Nicotiana tomentosiformis. Fluorescence in situ hybridization (FISH) and Southern blot analysis revealed its occurrence as an independent satellite (termed an A1/A2 satellite) outside of rDNA loci in species of Nicotiana section Tomentosae. The chromosomal location, patterns of genomic dispersion, and copy numbers of its tandemly arranged units varied between the species. In more distantly related Nicotiana species the A1/A2 repeats were found only at the nucleolar organizer regions (NOR). There was a trend toward the elimination of the A1/A2 satellite in N. tabacum (tobacco), an allotetraploid with parents closely related to the diploids N. sylvestris and N. tomentosiformis. This process may have already commenced in an S3 generation of synthetic tobacco. Cytosine residues in the IGS were significantly hypomethylated compared with the A1/A2 satellite. There was no clear separation between the IGS and satellite fractions in sequence analysis of individual clones and we found no evidence for CG suppression. Taken together the data indicate a dynamic nature of the A1/A2 repeats in Nicotiana genomes, with evidence for recurrent integration, copy number expansions, and contractions.
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Affiliation(s)
- K Y Lim
- School of Biological Sciences, University of London, London E1 4NS, United Kingdom
| | - K Skalicka
- Institute of Biophysics, AV CR, 612 65 Brno, Czech Republic
| | - B Koukalova
- Institute of Biophysics, AV CR, 612 65 Brno, Czech Republic
| | - R A Volkov
- Department of Genetics, Center of Plant Molecular Biology (ZMBP), 72076 Tübingen, Germany
| | - R Matyasek
- Institute of Biophysics, AV CR, 612 65 Brno, Czech Republic
| | - V Hemleben
- Department of Genetics, Center of Plant Molecular Biology (ZMBP), 72076 Tübingen, Germany
| | - A R Leitch
- School of Biological Sciences, University of London, London E1 4NS, United Kingdom
| | - A Kovarik
- Institute of Biophysics, AV CR, 612 65 Brno, Czech Republic
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24
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Macas J, Navrátilová A, Mészáros T. Sequence subfamilies of satellite repeats related to rDNA intergenic spacer are differentially amplified on Vicia sativa chromosomes. Chromosoma 2003; 112:152-8. [PMID: 14579131 DOI: 10.1007/s00412-003-0255-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2003] [Accepted: 08/06/2003] [Indexed: 10/26/2022]
Abstract
We cloned and sequenced the Vicia sativa 25S-18S rDNA intergenic spacer (IGS) and the satellite repeat S12, thought to be related to the spacer sequence. The spacer was shown to contain three types of subrepeats (A, B, and C) with monomers of 173 bp (A), 10 bp (B), and 66 bp (C), separated by unique or partially duplicated sequences. Two spacer variants were detected in V. sativa that differed in length (2990 and 3168 bp) owing to an extra copy of the subrepeat A. The A subrepeats were also shown to be highly homologous to the satellite repeat S12, which is located in large clusters on chromosomes 4, 5, and 6, and is not associated with the rDNA loci. Sequencing of additional S12 clones retrieved from a shotgun genomic library allowed definition of three subfamilies of this repeat based on minor differences in their nucleotide sequences. Two of these subfamilies could be discriminated from the rest of the S12 sequences as well as from the IGS A subrepeats using specific oligonucleotide primers that labeled only a subset of the S12 loci when used in the primed in situ DNA labeling (PRINS) reaction on mitotic chromosomes. These experiments showed that, in spite of the high overall similarity of the IGS A subrepeats and the S12 satellite repeats, there are S12 subfamilies that are divergent from the common consensus and are present at only some of the chromosomes containing the S12 loci. Thus, the subfamilies may have evolved at these loci following the spreading of the A subrepeats from the IGS to genomic regions outside the rDNA clusters.
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Affiliation(s)
- Jiri Macas
- Institute of Plant Molecular Biology, Laboratory of Molecular Cytogenetics, Branisovská 31, Ceské Budejovice, 37005 Czech Republic.
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25
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Manzanero S, Rutten T, Kotseruba V, Houben A. Alterations in the distribution of histone H3 phosphorylation in mitotic plant chromosomes in response to cold treatment and the protein phosphatase inhibitor cantharidin. Chromosome Res 2003; 10:467-76. [PMID: 12489829 DOI: 10.1023/a:1020940313841] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The function of the phosphorylation of histone H3 at Ser 10 in plant cell division is uncertain. The timing correlates with chromosome condensation, and studies in plant meiosis suggest that it is involved in sister chromatid cohesion. In mitosis, plant chromosomes are highly phosphorylated in the pericentromeric region only. In order to modulate H3 phosphorylation, root meristems of different plant species were treated with the protein phosphatase inhibitor cantharidin or with ice-water. Immunostaining using an antibody specific to phosphorylated H3 at Ser 10 revealed a high level of H3 phosphorylation along the whole mitotic chromosome after cantharidin treatment, which resembles the distribution seen exclusively in first meiotic division. In chromosomes that were isolated from meristems treated with ice-water, the heterochromatic regions and nucleolar organizer regions, in addition to the pericentromeric region, were highly phosphorylated at H3. Cantharidin and ice-water also affected spindle assembly and chromosome length, but these effects did not seem to be directly linked to changes in H3 phosphorylation.
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Affiliation(s)
- Silvia Manzanero
- Departamento de Genética, Facultad de Biología, Universidad Complutense, 28040 Madrid, Spain
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26
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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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27
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28
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Stupar RM, Song J, Tek AL, Cheng Z, Dong F, Jiang J. Highly condensed potato pericentromeric heterochromatin contains rDNA-related tandem repeats. Genetics 2002; 162:1435-44. [PMID: 12454086 PMCID: PMC1462313 DOI: 10.1093/genetics/162.3.1435] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The heterochromatin in eukaryotic genomes represents gene-poor regions and contains highly repetitive DNA sequences. The origin and evolution of DNA sequences in the heterochromatic regions are poorly understood. Here we report a unique class of pericentromeric heterochromatin consisting of DNA sequences highly homologous to the intergenic spacer (IGS) of the 18S.25S ribosomal RNA genes in potato. A 5.9-kb tandem repeat, named 2D8, was isolated from a diploid potato species Solanum bulbocastanum. Sequence analysis indicates that the 2D8 repeat is related to the IGS of potato rDNA. This repeat is associated with highly condensed pericentromeric heterochromatin at several hemizygous loci. The 2D8 repeat is highly variable in structure and copy number throughout the Solanum genus, suggesting that it is evolutionarily dynamic. Additional IGS-related repetitive DNA elements were also identified in the potato genome. The possible mechanism of the origin and evolution of the IGS-related repeats is discussed. We demonstrate that potato serves as an interesting model for studying repetitive DNA families because it is propagated vegetatively, thus minimizing the meiotic mechanisms that can remove novel DNA repeats.
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Affiliation(s)
- Robert M Stupar
- Department of Horticulture, University of Wisconsin, Madison 53706, USA
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29
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Castro J, Rodríguez S, Pardo BG, Sánchez L, Martínez P. Population analysis of an unusual NOR-site polymorphism in brown trout (Salmo trutta L.). Heredity (Edinb) 2001; 86:291-302. [PMID: 11488966 DOI: 10.1046/j.1365-2540.2001.00834.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A population analysis of an unusual NOR-site polymorphism previously detected in brown trout (Salmo trutta L.) from North-western Spain was carried out in 225 individuals from 20 native populations from this area. The analysis performed has permitted us to reveal: (i) the ubiquity of this phenomenon in most river basins from NW Spain, 13 extra-NORs not observed in standard trout being detected; (ii) the rDNA constitution of all extra-NORs, as confirmed by CMA3-staining and rDNA-FISH, and their capability to constitute their own nucleolus; (iii) the constant location of extra-NORs within individuals and their stable transmission across generations; and (iv) the telomeric location of Ag-NORs, which were randomly distributed in the karyotype of S. trutta, mostly in the heterozygous condition. Repetitive sequences in the IGS or scattered along rDNA units, rather than chromosome rearrangements, could play an important role in the dispersion of NORs. The polymorphism described seems to have a single geographical origin, since a positive correlation was demonstrated between the degree of polymorphism and geographical distance to a central point of the river basin where the phenomenon showed a higher intensity. The distribution of NOR-site variation as compared with allozyme variation in the populations studied, showed significant statistical differences. Selection against high copy number, or mutation due to changes in NOR location, could be acting on this polymorphism to explain the observed distribution. The high dispersion of NOR-site variants within and among populations suggests the transposition phenomenon responsible for NOR jumping could be still active.
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Affiliation(s)
- J Castro
- Departamento de Biología Fundamental, Area de Genética, Facultad de Veterinaria, Universidad de Santiago de Compostela, 27002 Lugo, Spain
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30
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Rousselet J, Monti L, Auger-Rozenberg MA, Parker JS, Lemeunier F. Chromosome fission associated with growth of ribosomal DNA in Neodiprion abietis (Hymenoptera: Diprionidae). Proc Biol Sci 2000; 267:1819-23. [PMID: 11052531 PMCID: PMC1690759 DOI: 10.1098/rspb.2000.1216] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The haploid complement consists of seven metacentric chromosomes in most diprionid species but has evolved to n = 8 by fission in Neodiprion abietis. This fission generated a small telocentric chromosome and a large pseudoacrocentric chromosome with a short arm carrying a satellite. In situ hybridization indicated that the location of the rRNA gene cluster corresponds to the whole short arm. This suggests that (i) the breaking point was located close to an rRNA gene cluster, and (ii) fission was associated with growth of rDNA. These results suggest rDNA as a preferential breaking point but with a role in the healing of naked chromosome ends.
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Affiliation(s)
- J Rousselet
- Laboratoire Populations, Génétique et Evolution, CNRS, Gif-sur-Yvette, France
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31
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32
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Fuchs J, Strehl S, Brandes A, Schweizer D, Schubert I. Molecular-cytogenetic characterization of the Vicia faba genome--heterochromatin differentiation, replication patterns and sequence localization. Chromosome Res 1998; 6:219-30. [PMID: 9609666 DOI: 10.1023/a:1009215802737] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
A comprehensive survey of the molecular-cytogenetic features of the Vicia faba chromosome complement (2n = 12) is given. It includes previous as well as new original data. Various Giemsa, restriction endonuclease and fluorochrome banding patterns, azacytidine-mediated segment extension, replication patterns, lateral A/T asymmetry and sequence localization data for tandemly arranged simple sequence repeats, dispersed repeats and coding sequences as well as histone acetylation patterns are considered. This allows not only to distinguish and characterize telomeres, subtelomeres, centromeres and the NOR, but also the structure of the 5S rRNA gene loci and two main types of interstitial heterochromatin. Additionally, it offers physical landmarks within euchromatic areas. Thus, the field bean genome, exemplified by the reconstructed karyotype ACB, belongs to the cytogenetically best investigated plant genomes.
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Affiliation(s)
- J Fuchs
- Institut für Pflanzengenetik und Kulturpflanzenforschung, Gatersleben, Germany
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33
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Abstract
A spontaneous chromosome fission in the plant Hypochoeris radicata has been characterized by Feulgen staining, in situ hybridization of the rDNA probe pTA71 and silver staining for active nucleolus organizing regions. The parental acrocentric chromosome has no detectable ribosomal genes at the centromere, but both fission derivatives possess active NORs at their centric ends. In fission heterozygotes, pachytene configurations studied by synaptonemal complex spreading show that the ribosomal cistrons form short arms on each telocentric which pair together to form a triradial. The paired short arms are associated with the single nucleolus at pachytene. It is proposed that the origin and stabilization of the fission rearrangement involved transposition of rDNA from the nucleolus organizing region of chromosome 3 into the centromeric region of chromosome 1.
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Affiliation(s)
- K J Hall
- Department of Botany, School of Plant Sciences, University of Reading, Whiteknights, UK
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