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Garcia S, Pascual-Díaz JP, Krumpolcová A, Kovarík A. Analysis of 5S rDNA Genomic Organization Through the RepeatExplorer2 Pipeline: A Simplified Protocol. Methods Mol Biol 2023; 2672:501-512. [PMID: 37335496 DOI: 10.1007/978-1-0716-3226-0_30] [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: 06/21/2023]
Abstract
The ribosomal RNA genes (rDNA) are universal genome components with a housekeeping function, given the crucial role of ribosomal RNA in the synthesis of ribosomes and thus for life-on-Earth. Therefore, their genomic organization is of considerable interest for biologists, in general. Ribosomal RNA genes have also been largely used to establish phylogenetic relationships, and to identify allopolyploid or homoploid hybridization.Here, we demonstrate how high-throughput sequencing data, through graph clustering implemented in RepeatExplorer2 pipeline ( https://repeatexplorer-elixir.cerit-sc.cz/galaxy/ ), can be helpful to decipher the genomic organization of 5S rRNA genes. We show that the linear shapes of cluster graphs are reminiscent to the linked organization of 5S and 35S rDNA (L-type arrangement) while the circular graphs correspond to their separate arrangement (S-type). We further present a simplified protocol based on the paper by (Garcia et al., Front Plant Sci 11:41, 2020) about the use of graph clustering of 5S rDNA homoeologs (S-type) to identify hybridization events in the species history. We found that the graph complexity (i.e., graph circularity in this case) is related to ploidy and genome complexity, with diploids typically showing circular-shaped graphs while allopolyploids and other interspecific hybrids display more complex graphs, with usually two or more interconnected loops representing intergenic spacers. When a three-genomic comparative clustering analysis from a given hybrid (homoploid/allopolyploid) and its putative progenitor species (diploids) is performed, it is possible to identify the corresponding homoeologous 5S rRNA gene families, and to elucidate the contribution of each putative parental genome to the 5S rDNA pool of the hybrid. Thus, the analysis of 5S rDNA cluster graphs by RepeatExplorer, together with information coming from other sources (e.g., morphology, cytogenetics) is a complementary approach for the determination of allopolyploid or homoploid hybridization and even ancient introgression events.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (CSIC - Ajuntament de Barcelona), Barcelona, Spain
| | | | - Alice Krumpolcová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ales Kovarík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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Tynkevich YO, Novikov AV, Chorney II, Volkov RA. Organization of the 5S rDNA Intergenic Spacer and Its Use in the Molecular Taxonomy of the Genus Aconitum L. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722060111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Fehrer J, Bertrand YJK, Hartmann M, Caklová P, Josefiová J, Bräutigam S, Chrtek J. A Multigene Phylogeny of Native American Hawkweeds ( Hieracium Subgen. Chionoracium, Cichorieae, Asteraceae): Origin, Speciation Patterns, and Migration Routes. PLANTS (BASEL, SWITZERLAND) 2022; 11:2584. [PMID: 36235450 PMCID: PMC9571344 DOI: 10.3390/plants11192584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/24/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Native American hawkweeds are mainly mountainous species that are distributed all over the New World. They are severely understudied with respect to their origin, colonization of the vast distribution area, and species relationships. Here, we attempt to reconstruct the evolutionary history of the group by applying seven molecular markers (plastid, nuclear ribosomal and low-copy genes). Phylogenetic analyses revealed that Chionoracium is a subgenus of the mainly Eurasian genus Hieracium, which originated from eastern European hawkweeds about 1.58-2.24 million years ago. Plastid DNA suggested a single origin of all Chionoracium species. They colonized the New World via Beringia and formed several distinct lineages in North America. Via one Central American lineage, the group colonized South America and radiated into more than a hundred species within about 0.8 million years, long after the closure of the Isthmus of Panama and the most recent uplift of the Andes. Despite some incongruences shown by different markers, most of them revealed the same crown groups of closely related taxa, which were, however, largely in conflict with traditional sectional classifications. We provide a basic framework for further elucidation of speciation patterns. A thorough taxonomic revision of Hieracium subgen. Chionoracium is recommended.
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Affiliation(s)
- Judith Fehrer
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
| | - Yann J. K. Bertrand
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
| | - Matthias Hartmann
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
- Department of Geobotany & Botanical Garden, Institute of Biology, Martin Luther University Halle-Wittenberg, 06108 Halle (Saale), Germany
- Thünen Institute of Biodiversity, Bundesallee 65, 38116 Braunschweig, Germany
| | - Petra Caklová
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
| | - Jiřina Josefiová
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
| | | | - Jindřich Chrtek
- Institute of Botany, Czech Academy of Sciences, 25243 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University, 12801 Prague, Czech Republic
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Tynkevich YO, Shelyfist AY, Kozub LV, Hemleben V, Panchuk II, Volkov RA. 5S Ribosomal DNA of Genus Solanum: Molecular Organization, Evolution, and Taxonomy. FRONTIERS IN PLANT SCIENCE 2022; 13:852406. [PMID: 35498650 PMCID: PMC9043955 DOI: 10.3389/fpls.2022.852406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
The Solanum genus, being one of the largest among high plants, is distributed worldwide and comprises about 1,200 species. The genus includes numerous agronomically important species such as Solanum tuberosum (potato), Solanum lycopersicum (tomato), and Solanum melongena (eggplant) as well as medical and ornamental plants. The huge Solanum genus is a convenient model for research in the field of molecular evolution and structural and functional genomics. Clear knowledge of evolutionary relationships in the Solanum genus is required to increase the effectiveness of breeding programs, but the phylogeny of the genus is still not fully understood. The rapidly evolving intergenic spacer region (IGS) of 5S rDNA has been successfully used for inferring interspecific relationships in several groups of angiosperms. Here, combining cloning and sequencing with bioinformatic analysis of genomic data available in the SRA database, we evaluate the molecular organization and diversity of IGS for 184 accessions, representing 137 species of the Solanum genus. It was found that the main mechanisms of IGS molecular evolution was step-wise accumulation of single base substitution or short indels, and that long indels and multiple base substitutions, which arose repeatedly during evolution, were mostly not conserved and eliminated. The reason for this negative selection seems to be association between indels/multiple base substitutions and pseudogenization of 5S rDNA. Comparison of IGS sequences allowed us to reconstruct the phylogeny of the Solanum genus. The obtained dendrograms are mainly congruent with published data: same major and minor clades were found. However, relationships between these clades and position of some species (S. cochoae, S. clivorum, S. macrocarpon, and S. spirale) were different from those of previous results and require further clarification. Our results show that 5S IGS represents a convenient molecular marker for phylogenetic studies on the Solanum genus. In particular, the simultaneous presence of several structural variants of rDNA in the genome enables the detection of reticular evolution, especially in the largest and economically most important sect. Petota. The origin of several polyploid species should be reconsidered.
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Affiliation(s)
- Yurij O. Tynkevich
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Antonina Y. Shelyfist
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Liudmyla V. Kozub
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Vera Hemleben
- Center of Plant Molecular Biology (ZMBP), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Irina I. Panchuk
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
- Center of Plant Molecular Biology (ZMBP), Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Roman A. Volkov
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
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Borowska-Zuchowska N, Senderowicz M, Trunova D, Kolano B. Tracing the Evolution of the Angiosperm Genome from the Cytogenetic Point of View. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11060784. [PMID: 35336666 PMCID: PMC8953110 DOI: 10.3390/plants11060784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 05/05/2023]
Abstract
Cytogenetics constitutes a branch of genetics that is focused on the cellular components, especially chromosomes, in relation to heredity and genome structure, function and evolution. The use of modern cytogenetic approaches and the latest microscopes with image acquisition and processing systems enables the simultaneous two- or three-dimensional, multicolour visualisation of both single-copy and highly-repetitive sequences in the plant genome. The data that is gathered using the cytogenetic methods in the phylogenetic background enable tracing the evolution of the plant genome that involve changes in: (i) genome sizes; (ii) chromosome numbers and morphology; (iii) the content of repetitive sequences and (iv) ploidy level. Modern cytogenetic approaches such as FISH using chromosome- and genome-specific probes have been widely used in studies of the evolution of diploids and the consequences of polyploidy. Nowadays, modern cytogenetics complements analyses in other fields of cell biology and constitutes the linkage between genetics, molecular biology and genomics.
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Stepanenko A, Chen G, Hoang PTN, Fuchs J, Schubert I, Borisjuk N. The Ribosomal DNA Loci of the Ancient Monocot Pistia stratiotes L. (Araceae) Contain Different Variants of the 35S and 5S Ribosomal RNA Gene Units. FRONTIERS IN PLANT SCIENCE 2022; 13:819750. [PMID: 35310643 PMCID: PMC8928438 DOI: 10.3389/fpls.2022.819750] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
The freshwater plant water lettuce (Pistia stratiotes L.) grows in warm climatic zones and is used for phytoremediation and biomass production. P. stratiotes belongs to the Araceae, an ecologically and structurally diverse early monocot family, but the phylogenetic relationships among Araceae members are poorly understood. Ribosomal DNAs (rDNAs), including the 35S and 5S rDNA, encode the RNA components of ribosomes and are widely used in phylogenetic and evolutionary studies of various plant taxa. Here, we comprehensively characterized the chromosomal locations and molecular organization of 35S and 5S rDNA genes in water lettuce using karyological and molecular methods. Fluorescence in situ hybridization revealed a single location for the 35S and 5S rDNA loci, each on a different pair of the species' 28 chromosomes. Molecular cloning and nucleotide sequencing of 35S rDNA of P. stratiotes, the first representative Araceae sensu stricto in which such a study was performed, displayed typical structural characteristics. The full-length repeat showed high sequence conservation of the regions producing the 18S, 5.8S, and 25S rRNAs and divergence of the internal transcribed spacers ITS1 and ITS2 as well as the large intergenic spacer (IGS). Alignments of the deduced sequence of 18S rDNA with the sequences available for other Araceae and representatives of other clades were used for phylogenetic analysis. Examination of 11 IGS sequences revealed significant intra-genomic length variability due to variation in subrepeat number, with four types of units detected within the 35S rDNA locus of the P. stratiotes genome (estimated size 407 Mb/1C). Similarly, the 5S rDNA locus harbors gene units comprising a conserved 119-bp sequence encoding 5S rRNA and two types of non-transcribed spacer (NTS) sequences. Type I was classified into four subtypes, which apparently originated via progressive loss of subrepeats within the duplicated NTS region containing the 3' part of the 5S rRNA gene. The minor Type II NTS is shorter than Type I and differs in nucleotide composition. Some DNA clones containing two or three consecutive 5S rDNA repeats harbored 5S rDNA genes with different types of NTSs, confirming the mosaic composition of the 5S rDNA locus.
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Affiliation(s)
- Anton Stepanenko
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake and Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, School of Life Sciences, Huaiyin Normal University, Huai’an, China
| | - Guimin Chen
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake and Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, School of Life Sciences, Huaiyin Normal University, Huai’an, China
| | - Phuong T. N. Hoang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Faculty of Biology, Dalat University, Đà Lạt, Vietnam
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nikolai Borisjuk
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake and Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture and Environmental Protection, School of Life Sciences, Huaiyin Normal University, Huai’an, China
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Tao X, Li M, Zhao T, Feng S, Zhang H, Wang L, Han J, Gao M, Lu K, Chen Q, Zhou B, Guan X. Neofunctionalization of a polyploidization-activated cotton long intergenic non-coding RNA DAN1 during drought stress regulation. PLANT PHYSIOLOGY 2021; 186:2152-2168. [PMID: 33871645 PMCID: PMC8331171 DOI: 10.1093/plphys/kiab179] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/31/2021] [Indexed: 05/26/2023]
Abstract
The genomic shock of whole-genome duplication (WGD) and hybridization introduces great variation into transcriptomes, for both coding and noncoding genes. An altered transcriptome provides a molecular basis for improving adaptation during the evolution of new species. The allotetraploid cotton, together with the putative diploid ancestor species compose a fine model for study the rapid gene neofunctionalization over the genome shock. Here we report on Drought-Associated Non-coding gene 1 (DAN1), a long intergenic noncoding RNA (lincRNA) that arose from the cotton progenitor A-diploid genome after hybridization and WGD events during cotton evolution. DAN1 in allotetraploid upland cotton (Gossypium hirsutum) is a drought-responsive lincRNA predominantly expressed in the nucleoplasm. Chromatin isolation by RNA purification profiling and electrophoretic mobility shift assay analysis demonstrated that GhDAN1 RNA can bind with DNA fragments containing AAAG motifs, similar to DNA binding with one zinc finger transcription factor binding sequences. The suppression of GhDAN1 mainly regulates genes with AAAG motifs in auxin-response pathways, which are associated with drought stress regulation. As a result, GhDAN1-silenced plants exhibit improved tolerance to drought stress. This phenotype resembles the drought-tolerant phenotype of the A-diploid cotton ancestor species, which has an undetectable expression of DAN1. The role of DAN1 in cotton evolution and drought tolerance regulation suggests that the genomic shock of interspecific hybridization and WGD stimulated neofunctionalization of non-coding genes during the natural evolutionary process.
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Affiliation(s)
- Xiaoyuan Tao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Menglin Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ting Zhao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Shouli Feng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hailin Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Luyao Wang
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Center of Ministry of Cotton Education, Urumqi 830052, China
| | - Jin Han
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Mengtao Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kening Lu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Quanjia Chen
- College of Agriculture, Xinjiang Agricultural University, Engineering Research Center of Ministry of Cotton Education, Urumqi 830052, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xueying Guan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
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Chen G, Stepanenko A, Borisjuk N. Mosaic Arrangement of the 5S rDNA in the Aquatic Plant Landoltia punctata (Lemnaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:678689. [PMID: 34249048 PMCID: PMC8264772 DOI: 10.3389/fpls.2021.678689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/31/2021] [Indexed: 06/13/2023]
Abstract
Duckweeds are a group of monocotyledonous aquatic plants in the Araceae superfamily, represented by 37 species divided into five genera. Duckweeds are the fastest growing flowering plants and are distributed around the globe; moreover, these plants have multiple applications, including biomass production, wastewater remediation, and making pharmaceutical proteins. Dotted duckweed (Landoltia punctata), the sole species in genus Landoltia, is one of the most resilient duckweed species. The ribosomal DNA (rDNA) encodes the RNA components of ribosomes and represents a significant part of plant genomes but has not been comprehensively studied in duckweeds. Here, we characterized the 5S rDNA genes in L. punctata by cloning and sequencing 25 PCR fragments containing the 5S rDNA repeats. No length variation was detected in the 5S rDNA gene sequence, whereas the nontranscribed spacer (NTS) varied from 151 to 524 bp. The NTS variants were grouped into two major classes, which differed both in nucleotide sequence and the type and arrangement of the spacer subrepeats. The dominant class I NTS, with a characteristic 12-bp TC-rich sequence present in 3-18 copies, was classified into four subclasses, whereas the minor class II NTS, with shorter, 9-bp nucleotide repeats, was represented by two identical sequences. In addition to these diverse subrepeats, class I and class II NTSs differed in their representation of cis-elements and the patterns of predicted G-quadruplex structures, which may influence the transcription of the 5S rDNA. Similar to related duckweed species in the genus Spirodela, L. punctata has a relatively low rDNA copy number, but in contrast to Spirodela and the majority of other plants, the arrangement of the 5S rDNA units demonstrated an unusual, heterogeneous pattern in L. punctata, as revealed by analyzing clones containing double 5S rDNA neighboring units. Our findings may further stimulate the research on the evolution of the plant rDNA and discussion of the molecular forces driving homogenization of rDNA repeats in concerted evolution.
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Affiliation(s)
- Guimin Chen
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Anton Stepanenko
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
| | - Nikolai Borisjuk
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology Around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai’an, China
- Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai’an, China
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Krak K, Caklová P, Kopecký D, Blattner FR, Mahelka V. Horizontally Acquired nrDNAs Persist in Low Amounts in Host Hordeum Genomes and Evolve Independently of Native nrDNA. FRONTIERS IN PLANT SCIENCE 2021; 12:672879. [PMID: 34079572 PMCID: PMC8165317 DOI: 10.3389/fpls.2021.672879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Nuclear ribosomal DNA (nrDNA) has displayed extraordinary dynamics during the evolution of plant species. However, the patterns and evolutionary significance of nrDNA array expansion or contraction are still relatively unknown. Moreover, only little is known of the fate of minority nrDNA copies acquired between species via horizontal transfer. The barley genus Hordeum (Poaceae) represents a good model for such a study, as species of section Stenostachys acquired nrDNA via horizontal transfer from at least five different panicoid genera, causing long-term co-existence of native (Hordeum-like) and non-native (panicoid) nrDNAs. Using quantitative PCR, we investigated copy number variation (CNV) of nrDNA in the diploid representatives of the genus Hordeum. We estimated the copy number of the foreign, as well as of the native ITS types (ribotypes), and followed the pattern of their CNV in relation to the genus' phylogeny, species' genomes size and the number of nrDNA loci. For the native ribotype, we encountered an almost 19-fold variation in the mean copy number among the taxa analysed, ranging from 1689 copies (per 2C content) in H. patagonicum subsp. mustersii to 31342 copies in H. murinum subsp. glaucum. The copy numbers did not correlate with any of the genus' phylogeny, the species' genome size or the number of nrDNA loci. The CNV was high within the recognised groups (up to 13.2 × in the American I-genome species) as well as between accessions of the same species (up to 4×). Foreign ribotypes represent only a small fraction of the total number of nrDNA copies. Their copy numbers ranged from single units to tens and rarely hundreds of copies. They amounted, on average, to between 0.1% (Setaria ribotype) and 1.9% (Euclasta ribotype) of total nrDNA. None of the foreign ribotypes showed significant differences with respect to phylogenetic groups recognised within the sect. Stenostachys. Overall, no correlation was found between copy numbers of native and foreign nrDNAs suggesting the sequestration and independent evolution of native and non-native nrDNA arrays. Therefore, foreign nrDNA in Hordeum likely poses a dead-end by-product of horizontal gene transfer events.
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Affiliation(s)
- Karol Krak
- Czech Academy of Sciences, Institute of Botany, Prùhonice, Czechia
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague 6, Czechia
| | - Petra Caklová
- Czech Academy of Sciences, Institute of Botany, Prùhonice, Czechia
| | - David Kopecký
- Czech Academy of Sciences, Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Frank R. Blattner
- Experimental Taxonomy, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- German Centre of Integrative Biodiversity Research (iDiv) Halle–Jena–Leipzig, Leipzig, Germany
| | - Václav Mahelka
- Czech Academy of Sciences, Institute of Botany, Prùhonice, Czechia
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Vozárová R, Herklotz V, Kovařík A, Tynkevich YO, Volkov RA, Ritz CM, Lunerová J. Ancient Origin of Two 5S rDNA Families Dominating in the Genus Rosa and Their Behavior in the Canina-Type Meiosis. FRONTIERS IN PLANT SCIENCE 2021; 12:643548. [PMID: 33763100 PMCID: PMC7984461 DOI: 10.3389/fpls.2021.643548] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/15/2021] [Indexed: 05/02/2023]
Abstract
The genus Rosa comprises more than 100 woody species characterized by intensive hybridization, introgression, and an overall complex evolutionary history. Besides many diploid species (2n = 2x = 14) polyploids ranging from 3x to 10x are frequently found. Here we analyzed 5S ribosomal DNA in 19 species covering two subgenera and the major sections within subg. Rosa. In addition to diploids and polyploids with regular meiosis, we focused on 5x dogroses (Rosa sect. Caninae), which exhibit an asymmetric meiosis differentiating between bivalent- and univalent-forming chromosomes. Using genomic resources, we reconstructed 5S rDNA units to reveal their phylogenetic relationships. Additionally, we designed locus-specific probes derived from intergenic spacers (IGSs) and determined the position and number of 5S rDNA families on chromosomes. Two major 5S rDNA families (termed 5S_A and 5S_B, respectively) were found at variable ratios in both diploid and polyploid species including members of the early diverging subgenera, Rosa persica and Rosa minutifolia. Within subg. Rosa species of sect. Rosa amplified the 5S_A variant only, while taxa of other sections contained both variants at variable ratios. The 5S_B family was often co-localized with 35S rDNA at the nucleolar organizer regions (NOR) chromosomes, whereas the co-localization of the 5S_A family with NOR was only exceptionally observed. The allo-pentaploid dogroses showed a distinct distribution of 5S rDNA families between bivalent- and univalent-forming chromosomes. In conclusion, two divergent 5S rDNA families dominate rose genomes. Both gene families apparently arose in the early history of the genus, already 30 myrs ago, and apparently survived numerous speciation events thereafter. These observations are consistent with a relatively slow genome turnover in the Rosa genus.
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Affiliation(s)
- Radka Vozárová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Veit Herklotz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Yuri O. Tynkevich
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Roman A. Volkov
- Department of Molecular Genetics and Biotechnology, Yuriy Fedkovych Chernivtsi National University, Chernivtsi, Ukraine
| | - Christiane M. Ritz
- Department of Botany, Senckenberg Museum of Natural History Görlitz, Görlitz, Germany
- Chair of Biodiversity of Higher Plants, International Institute (IHI) Zittau, Technische Universität Dresden, Zittau, Germany
| | - Jana Lunerová
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
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Fehrer J, Slavíková R, Paštová L, Josefiová J, Mráz P, Chrtek J, Bertrand YJK. Molecular Evolution and Organization of Ribosomal DNA in the Hawkweed Tribe Hieraciinae (Cichorieae, Asteraceae). FRONTIERS IN PLANT SCIENCE 2021; 12:647375. [PMID: 33777082 PMCID: PMC7994888 DOI: 10.3389/fpls.2021.647375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/19/2021] [Indexed: 05/14/2023]
Abstract
Molecular evolution of ribosomal DNA can be highly dynamic. Hundreds to thousands of copies in the genome are subject to concerted evolution, which homogenizes sequence variants to different degrees. If well homogenized, sequences are suitable for phylogeny reconstruction; if not, sequence polymorphism has to be handled appropriately. Here we investigate non-coding rDNA sequences (ITS/ETS, 5S-NTS) along with the chromosomal organization of their respective loci (45S and 5S rDNA) in diploids of the Hieraciinae. The subtribe consists of genera Hieracium, Pilosella, Andryala, and Hispidella and has a complex evolutionary history characterized by ancient intergeneric hybridization, allele sharing among species, and incomplete lineage sorting. Direct or cloned Sanger sequences and phased alleles derived from Illumina genome sequencing were subjected to phylogenetic analyses. Patterns of homogenization and tree topologies based on the three regions were compared. In contrast to most other plant groups, 5S-NTS sequences were generally better homogenized than ITS and ETS sequences. A novel case of ancient intergeneric hybridization between Hispidella and Hieracium was inferred, and some further incongruences between the trees were found, suggesting independent evolution of these regions. In some species, homogenization of ITS/ETS and 5S-NTS sequences proceeded in different directions although the 5S rDNA locus always occurred on the same chromosome with one 45S rDNA locus. The ancestral rDNA organization in the Hieraciinae comprised 4 loci of 45S rDNA in terminal positions and 2 loci of 5S rDNA in interstitial positions per diploid genome. In Hieracium, some deviations from this general pattern were found (3, 6, or 7 loci of 45S rDNA; three loci of 5S rDNA). Some of these deviations concerned intraspecific variation, and most of them occurred at the tips of the tree or independently in different lineages. This indicates that the organization of rDNA loci is more dynamic than the evolution of sequences contained in them and that locus number is therefore largely unsuitable to inform about species relationships in Hieracium. No consistent differences in the degree of sequence homogenization and the number of 45S rDNA loci were found, suggesting interlocus concerted evolution.
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Affiliation(s)
- Judith Fehrer
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- *Correspondence: Judith Fehrer,
| | - Renáta Slavíková
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | | | - Jiřina Josefiová
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
| | - Patrik Mráz
- Department of Botany, Charles University, Prague, Czechia
| | - Jindřich Chrtek
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Charles University, Prague, Czechia
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Garcia S, Wendel JF, Borowska-Zuchowska N, Aïnouche M, Kuderova A, Kovarik A. The Utility of Graph Clustering of 5S Ribosomal DNA Homoeologs in Plant Allopolyploids, Homoploid Hybrids, and Cryptic Introgressants. FRONTIERS IN PLANT SCIENCE 2020; 11:41. [PMID: 32117380 PMCID: PMC7025596 DOI: 10.3389/fpls.2020.00041] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/13/2020] [Indexed: 05/18/2023]
Abstract
INTRODUCTION Ribosomal DNA (rDNA) loci have been widely used for identification of allopolyploids and hybrids, although few of these studies employed high-throughput sequencing data. Here we use graph clustering implemented in the RepeatExplorer (RE) pipeline to analyze homoeologous 5S rDNA arrays at the genomic level searching for hybridogenic origin of species. Data were obtained from more than 80 plant species, including several well-defined allopolyploids and homoploid hybrids of different evolutionary ages and from widely dispersed taxonomic groups. RESULTS (i) Diploids show simple circular-shaped graphs of their 5S rDNA clusters. In contrast, most allopolyploids and other interspecific hybrids exhibit more complex graphs composed of two or more interconnected loops representing intergenic spacers (IGS). (ii) There was a relationship between graph complexity and locus numbers. (iii) The sequences and lengths of the 5S rDNA units reconstituted in silico from k-mers were congruent with those experimentally determined. (iv) Three-genomic comparative cluster analysis of reads from allopolyploids and progenitor diploids allowed identification of homoeologous 5S rRNA gene families even in relatively ancient (c. 1 Myr) Gossypium and Brachypodium allopolyploids which already exhibit uniparental partial loss of rDNA repeats. (v) Finally, species harboring introgressed genomes exhibit exceptionally complex graph structures. CONCLUSION We found that the cluster graph shapes and graph parameters (k-mer coverage scores and connected component index) well-reflect the organization and intragenomic homogeneity of 5S rDNA repeats. We propose that the analysis of 5S rDNA cluster graphs computed by the RE pipeline together with the cytogenetic analysis might be a reliable approach for the determination of the hybrid or allopolyploid plant species parentage and may also be useful for detecting historical introgression events.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (IBB, CSIC - Ajuntament de Barcelona), Barcelona, Spain
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Jonathan F. Wendel
- Department of Ecology, Evolution & Organismal Biology, Iowa State University, Ames, IA, United States
| | - Natalia Borowska-Zuchowska
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Malika Aïnouche
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, Rennes, France
| | - Alena Kuderova
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Ales Kovarik
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
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Pamponét VCC, Souza MM, Silva GS, Micheli F, de Melo CAF, de Oliveira SG, Costa EA, Corrêa RX. Low coverage sequencing for repetitive DNA analysis in Passiflora edulis Sims: citogenomic characterization of transposable elements and satellite DNA. BMC Genomics 2019; 20:262. [PMID: 30940088 PMCID: PMC6444444 DOI: 10.1186/s12864-019-5576-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 02/28/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The cytogenomic study of repetitive regions is fundamental for the understanding of morphofunctional mechanisms and genome evolution. Passiflora edulis a species of relevant agronomic value, this work had its genome sequenced by next generation sequencing and bioinformatics analysis performed by RepeatExplorer pipeline. The clusters allowed the identification and characterization of repetitive elements (predominant contributors to most plant genomes). The aim of this study was to identify, characterize and map the repetitive DNA of P. edulis, providing important cytogenomic markers, especially sequences associated with the centromere. RESULTS Three clusters of satellite DNAs (69, 118 and 207) and seven clusters of Long Terminal Repeat (LTR) retrotransposons of the superfamilies Ty1/Copy and Ty3/Gypsy and families Angela, Athila, Chromovirus and Maximus-Sire (6, 11, 36, 43, 86, 94 and 135) were characterized and analyzed. The chromosome mapping of satellite DNAs showed two hybridization sites co-located in the 5S rDNA region (PeSat_1), subterminal hybridizations (PeSat_3) and hybridization in four sites, co-located in the 45S rDNA region (PeSat_2). Most of the retroelements hybridizations showed signals scattered in the chromosomes, diverging in abundance, and only the cluster 6 presented pericentromeric regions marking. No satellite DNAs and retroelement associated with centromere was observed. CONCLUSION P. edulis has a highly repetitive genome, with the predominance of Ty3/Gypsy LTR retrotransposon. The satellite DNAs and LTR retrotransposon characterized are promising markers for investigation of the evolutionary patterns and genetic distinction of species and hybrids of Passiflora.
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MESH Headings
- Chromosome Mapping
- Chromosomes, Plant
- DNA, Plant/genetics
- DNA, Plant/metabolism
- DNA, Satellite/classification
- DNA, Satellite/genetics
- High-Throughput Nucleotide Sequencing
- In Situ Hybridization, Fluorescence
- Passiflora/genetics
- Phylogeny
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 5S/genetics
- Retroelements/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Vanessa Carvalho Cayres Pamponét
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), km 16, Salobrinho, Ilhéus, Bahia CEP 45662-900 Brazil
| | - Margarete Magalhães Souza
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), km 16, Salobrinho, Ilhéus, Bahia CEP 45662-900 Brazil
| | - Gonçalo Santos Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), km 16, Salobrinho, Ilhéus, Bahia CEP 45662-900 Brazil
| | - Fabienne Micheli
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), km 16, Salobrinho, Ilhéus, Bahia CEP 45662-900 Brazil
- CIRAD, UMR AGAP, F-34398 Montpellier, France
| | - Cláusio Antônio Ferreira de Melo
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), km 16, Salobrinho, Ilhéus, Bahia CEP 45662-900 Brazil
| | - Sarah Gomes de Oliveira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Rua do Matão, 14 – Butantã, São Paulo, SP CEP 05508-090 Brazil
| | - Eduardo Almeida Costa
- Núcleo de Biologia Computacional e Gestão de Informações Biotecnológicas (NBCGIB), Universidade Estadual de Santa Cruz (UESC), km 16, Salobrinho, Ilhéus, Bahia CEP 45662-900 Brazil
| | - Ronan Xavier Corrêa
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), km 16, Salobrinho, Ilhéus, Bahia CEP 45662-900 Brazil
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Grover CE, Arick MA, Thrash A, Conover JL, Sanders WS, Peterson DG, Frelichowski JE, Scheffler JA, Scheffler BE, Wendel JF. Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing. Genome Biol Evol 2019; 11:53-71. [PMID: 30476109 PMCID: PMC6320677 DOI: 10.1093/gbe/evy256] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2018] [Indexed: 12/24/2022] Open
Abstract
We employed phylogenomic methods to study molecular evolutionary processes and phylogeny in the geographically widely dispersed New World diploid cottons (Gossypium, subg. Houzingenia). Whole genome resequencing data (average of 33× genomic coverage) were generated to reassess the phylogenetic history of the subgenus and provide a temporal framework for its diversification. Phylogenetic analyses indicate that the subgenus likely originated following transoceanic dispersal from Africa about 6.6 Ma, but that nearly all of the biodiversity evolved following rapid diversification in the mid-Pleistocene (0.5-2.0 Ma), with multiple long-distance dispersals required to account for range expansion to Arizona, the Galapagos Islands, and Peru. Comparative analyses of cpDNAversus nuclear data indicate that this history was accompanied by several clear cases of interspecific introgression. Repetitive DNAs contribute roughly half of the total 880 Mb genome, but most transposable element families are relatively old and stable among species. In the genic fraction, pairwise synonymous mutation rates average 1% per Myr, with nonsynonymous changes being about seven times less frequent. Over 1.1 million indels were detected and phylogenetically polarized, revealing a 2-fold bias toward deletions over small insertions. We suggest that this genome down-sizing bias counteracts genome size growth by TE amplification and insertions, and helps explain the relatively small genomes that are restricted to this subgenus. Compared with the rate of nucleotide substitution, the rate of indel occurrence is much lower averaging about 17 nucleotide substitutions per indel event.
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Affiliation(s)
- Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | - Mark A Arick
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University
| | - Adam Thrash
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University
| | - Justin L Conover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | - William S Sanders
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University
- Department of Computer Science & Engineering, Mississippi State University
- The Jackson Laboratory, Connecticut
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University
| | | | | | - Brian E Scheffler
- USDA, Genomics and Bioinformatics Research Unit, Stoneville, Mississippi
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
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15
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Joachimiak AJ, Hasterok R, Sliwinska E, Musiał K, Grabowska-Joachimiak A. FISH-aimed karyotype analysis in Aconitum subgen. Aconitum reveals excessive rDNA sites in tetraploid taxa. PROTOPLASMA 2018; 255. [PMID: 29541843 PMCID: PMC6133112 DOI: 10.1007/s00709-018-1238-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The location of 5S and 35S rDNA sequences in chromosomes of four Aconitum subsp. Aconitum species was analyzed after fluorescence in situ hybridization (FISH). Both in diploids (2n = 2x = 16; Aconitum variegatum, A. degenii) and tetraploids (2n = 4× = 32; A. firmum, A. plicatum), rDNA repeats were localized exclusively on the shorter arms of chromosomes, in subterminal or pericentromeric sites. All analyzed species showed similar basal genome size (Cx = 5.31-5.71 pg). The most striking features of tetraploid karyotypes were the conservation of diploid rDNA loci and emergence of many additional 5S rDNA clusters. Chromosomal distribution of excessive ribosomal sites suggests their role in the secondary diploidization of tetraploid karyotypes.
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Affiliation(s)
- Andrzej J Joachimiak
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Gronostajowa 9, PL-30-387, Kraków, Poland.
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, University of Silesia in Katowice, Jagiellonska 28, 40-032, Katowice, Poland
| | - Elwira Sliwinska
- Laboratory of Molecular Biology and Cytometry, Department of Plant Genetics and Biotechnology, University of Technology and Life Sciences in Bydgoszcz, Kaliskiego 7, 85-789, Bydgoszcz, Poland
| | - Krystyna Musiał
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Gronostajowa 9, PL-30-387, Kraków, Poland
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16
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Fadl-Allah E, Mahmoud MH, Abd El-Twab M, Helmey R. Aflatoxin B1induces chromosomal aberrations and 5S rDNA alterations in durum wheat. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.jaubas.2011.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- E.M. Fadl-Allah
- Botany Department, Faculty of Science, Minia University, Egypt
| | - M.A-H. Mahmoud
- Genetics Department, Faculty of Agriculture, Minia University, Egypt
| | | | - R.K. Helmey
- Botany Department, Faculty of Science, Minia University, Egypt
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17
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High and uneven levels of 45S rDNA site-number variation across wild populations of a diploid plant genus (Anacyclus, Asteraceae). PLoS One 2017; 12:e0187131. [PMID: 29088249 PMCID: PMC5663423 DOI: 10.1371/journal.pone.0187131] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/13/2017] [Indexed: 12/13/2022] Open
Abstract
The nuclear genome harbours hundreds to several thousand copies of ribosomal DNA. Despite their essential role in cellular ribogenesis few studies have addressed intrapopulation, interpopulation and interspecific levels of rDNA variability in wild plants. Some studies have assessed the extent of rDNA variation at the sequence and copy-number level with large sampling in several species. However, comparable studies on rDNA site number variation in plants, assessed with extensive hierarchical sampling at several levels (individuals, populations, species) are lacking. In exploring the possible causes for ribosomal loci dynamism, we have used the diploid genus Anacyclus (Asteraceae) as a suitable system to examine the evolution of ribosomal loci. To this end, the number and chromosomal position of 45S rDNA sites have been determined in 196 individuals from 47 populations in all Anacyclus species using FISH. The 45S rDNA site-number has been assessed in a significant sample of seed plants, which usually exhibit rather consistent features, except for polyploid plants. In contrast, the level of rDNA site-number variation detected in Anacyclus is outstanding in the context of angiosperms particularly regarding populations of the same species. The number of 45S rDNA sites ranged from four to 11, accounting for 14 karyological ribosomal phenotypes. Our results are not even across species and geographical areas, and show that there is no clear association between the number of 45S rDNA loci and the life cycle in Anacyclus. A single rDNA phenotype was detected in several species, but a more complex pattern that included intra-specific and intra-population polymorphisms was recorded in A. homogamos, A. clavatus and A. valentinus, three weedy species showing large and overlapping distribution ranges. It is likely that part of the cytogenetic changes and inferred dynamism found in these species have been triggered by genomic rearrangements resulting from contemporary hybridisation.
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18
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Ye L, Zhang C, Tang X, Chen Y, Liu S. Variations in 5S rDNAs in diploid and tetraploid offspring of red crucian carp × common carp. BMC Genet 2017; 18:75. [PMID: 28789633 PMCID: PMC5549377 DOI: 10.1186/s12863-017-0542-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 08/02/2017] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The allotetraploid hybrid fish (4nAT) that was created in a previous study through an intergeneric cross between red crucian carp (Carassius auratus red var., ♀) and common carp (Cyprinus carpio L., ♂) provided an excellent platform to investigate the effect of hybridization and polyploidization on the evolution of 5S rDNA. The 5S rDNAs of paternal common carp were made up of a coding sequence (CDS) and a non-transcribed spacer (NTS) unit, and while the 5S rDNAs of maternal red crucian carp contained a CDS and a NTS unit, they also contained a variable number of interposed regions (IPRs). The CDSs of the 5S rDNAs in both parental fishes were conserved, while their NTS units seemed to have been subjected to rapid evolution. RESULTS The diploid hybrid 2nF1 inherited all the types of 5S rDNAs in both progenitors and there were no signs of homeologous recombination in the 5S rDNAs of 2nF1 by sequencing of PCR products. We obtained two segments of 5S rDNA with a total length of 16,457 bp from allotetraploid offspring 4nAT through bacterial artificial chromosome (BAC) sequencing. Using this sequence together with the 5S rDNA sequences amplified from the genomic DNA of 4nAT, we deduced that the 5S rDNAs of 4nAT might be inherited from the maternal progenitor red crucian carp. Additionally, the IPRs in the 5S rDNAs of 4nAT contained A-repeats and TA-repeats, which was not the case for the IPRs in the 5S rDNAs of 2nF1. We also detected two signals of a 200-bp fragment of 5S rDNA in the chromosomes of parental progenitors and hybrid progenies by fluorescence in situ hybridization (FISH). CONCLUSIONS We deduced that during the evolution of 5S rDNAs in different ploidy hybrid fishes, interlocus gene conversion events and tandem repeat insertion events might occurred in the process of polyploidization. This study provided new insights into the relationship among the evolution of 5S rDNAs, hybridization and polyploidization, which were significant in clarifying the genome evolution of polyploid fish.
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Affiliation(s)
- Lihai Ye
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Xiaojun Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yiyi Chen
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
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Garcia S, Kovařík A, Leitch AR, Garnatje T. Cytogenetic features of rRNA genes across land plants: analysis of the Plant rDNA database. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:1020-1030. [PMID: 27943584 DOI: 10.1111/tpj.13442] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 11/22/2016] [Accepted: 11/24/2016] [Indexed: 05/09/2023]
Abstract
The online resource http://www.plantrdnadatabase.com/ stores information on the number, chromosomal locations and structure of the 5S and 18S-5.8S-26S (35S) ribosomal DNAs (rDNA) in plants. This resource was exploited to study relationships between rDNA locus number, distribution, the occurrence of linked (L-type) and separated (S-type) 5S and 35S rDNA units, chromosome number, genome size and ploidy level. The analyses presented summarise current knowledge on rDNA locus numbers and distribution in plants. We analysed 2949 karyotypes, from 1791 species and 86 plant families, and performed ancestral character state reconstructions. The ancestral karyotype (2n = 16) has two terminal 35S sites and two interstitial 5S sites, while the median (2n = 24) presents four terminal 35S sites and three interstitial 5S sites. Whilst 86.57% of karyotypes show S-type organisation (ancestral condition), the L-type arrangement has arisen independently several times during plant evolution. A non-terminal position of 35S rDNA was found in about 25% of single-locus karyotypes, suggesting that terminal locations are not essential for functionality and expression. Single-locus karyotypes are very common, even in polyploids. In this regard, polyploidy is followed by subsequent locus loss. This results in a decrease in locus number per monoploid genome, forming part of the diploidisation process returning polyploids to a diploid-like state over time.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
| | - Ales Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, Brno, 612 65, Czech Republic
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB-CSIC-ICUB), Passeig del Migdia s/n, 08038, Barcelona, Catalonia, Spain
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20
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Totta C, Rosato M, Ferrer-Gallego P, Lucchese F, Rosselló JA. Temporal frames of 45S rDNA site-number variation in diploid plant lineages: lessons from the rock rose genusCistus(Cistaceae). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Chiara Totta
- Università degli Studi Roma Tre; Viale G. Marconi 446 00146 Rome Italy
| | - Marcela Rosato
- Jardín Botánico-ICBiBE-Unidad Asociada CSIC; Universidad de Valencia; c/Quart 80 E46008 Valencia Spain
| | - Pablo Ferrer-Gallego
- CIEF, Servicio de Vida Silvestre; Generalitat Valenciana; Avda. Comarques del País Valencià 114 E46930 Valencia Spain
| | - Fernando Lucchese
- Università degli Studi Roma Tre; Viale G. Marconi 446 00146 Rome Italy
| | - Josep A. Rosselló
- Jardín Botánico-ICBiBE-Unidad Asociada CSIC; Universidad de Valencia; c/Quart 80 E46008 Valencia Spain
- Carl Faust Fdn.; PO Box 112 E17300 Blanes Spain
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Rosato M, Kovařík A, Garilleti R, Rosselló JA. Conserved Organisation of 45S rDNA Sites and rDNA Gene Copy Number among Major Clades of Early Land Plants. PLoS One 2016; 11:e0162544. [PMID: 27622766 PMCID: PMC5021289 DOI: 10.1371/journal.pone.0162544] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 08/24/2016] [Indexed: 11/26/2022] Open
Abstract
Genes encoding ribosomal RNA (rDNA) are universal key constituents of eukaryotic genomes, and the nuclear genome harbours hundreds to several thousand copies of each species. Knowledge about the number of rDNA loci and gene copy number provides information for comparative studies of organismal and molecular evolution at various phylogenetic levels. With the exception of seed plants, the range of 45S rDNA locus (encoding 18S, 5.8S and 26S rRNA) and gene copy number variation within key evolutionary plant groups is largely unknown. This is especially true for the three earliest land plant lineages Marchantiophyta (liverworts), Bryophyta (mosses), and Anthocerotophyta (hornworts). In this work, we report the extent of rDNA variation in early land plants, assessing the number of 45S rDNA loci and gene copy number in 106 species and 25 species, respectively, of mosses, liverworts and hornworts. Unexpectedly, the results show a narrow range of ribosomal locus variation (one or two 45S rDNA loci) and gene copies not present in vascular plant lineages, where a wide spectrum is recorded. Mutation analysis of whole genomic reads showed higher (3-fold) intragenomic heterogeneity of Marchantia polymorpha (Marchantiophyta) rDNA compared to Physcomitrella patens (Bryophyta) and two angiosperms (Arabidopsis thaliana and Nicotiana tomentosifomis) suggesting the presence of rDNA pseudogenes in its genome. No association between phylogenetic position, taxonomic adscription and the number of rDNA loci and gene copy number was found. Our results suggest a likely evolutionary rDNA stasis during land colonisation and diversification across 480 myr of bryophyte evolution. We hypothesise that strong selection forces may be acting against ribosomal gene locus amplification. Despite showing a predominant haploid phase and infrequent meiosis, overall rDNA homogeneity is not severely compromised in bryophytes.
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Affiliation(s)
- Marcela Rosato
- Jardín Botánico, ICBiBE-Unidad Asociada CSIC, Universidad de Valencia, c/Quart 80, E-46008, Valencia, Spain
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ–61265, Czech Republic
| | - Ricardo Garilleti
- Departamento de Botánica, Facultad de Farmacia, Universidad de Valencia, E-46100, Burjassot, Spain
| | - Josep A. Rosselló
- Jardín Botánico, ICBiBE-Unidad Asociada CSIC, Universidad de Valencia, c/Quart 80, E-46008, Valencia, Spain
- Marimurtra Bot. Garden, Carl Faust Fdn., PO Box 112, E-17300, Blanes, Catalonia, Spain
- * E-mail:
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Wang W, Ma L, Becher H, Garcia S, Kovarikova A, Leitch IJ, Leitch AR, Kovarik A. Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb. Chromosoma 2015; 125:683-99. [PMID: 26637996 PMCID: PMC5023732 DOI: 10.1007/s00412-015-0556-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 11/05/2015] [Indexed: 11/28/2022]
Abstract
In all eukaryotes, the highly repeated 35S ribosomal DNA (rDNA) sequences encoding 18S-5.8S-26S ribosomal RNA (rRNA) typically show high levels of intragenomic uniformity due to homogenisation processes, leading to concerted evolution of 35S rDNA repeats. Here, we compared 35S rDNA divergence in several seed plants using next generation sequencing and a range of molecular and cytogenetic approaches. Most species showed similar 35S rDNA homogeneity indicating concerted evolution. However, Cycas revoluta exhibits an extraordinary diversity of rDNA repeats (nucleotide sequence divergence of different copies averaging 12 %), influencing both the coding and non-coding rDNA regions nearly equally. In contrast, its rRNA transcriptome was highly homogeneous suggesting that only a minority of genes (<20 %) encode functional rRNA. The most common SNPs were C > T substitutions located in symmetrical CG and CHG contexts which were also highly methylated. Both functional genes and pseudogenes appear to cluster on chromosomes. The extraordinary high levels of 35S rDNA diversity in C. revoluta, and probably other species of cycads, indicate that the frequency of repeat homogenisation has been much lower in this lineage, compared with all other land plant lineages studied. This has led to the accumulation of methylation-driven mutations and pseudogenisation. Potentially, the reduced homology between paralogs prevented their elimination by homologous recombination, resulting in long-term retention of rDNA pseudogenes in the genome.
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Affiliation(s)
- Wencai Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Lu Ma
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Hannes Becher
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Sònia Garcia
- Laboratori de Botànica-Unitat associada CSIC, Facultat de Farmàcia, Universitat de Barcelona, 08028, Barcelona, Catalonia, Spain
| | - Alena Kovarikova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic.
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Re-evaluating the phylogeny of allopolyploid Gossypium L. Mol Phylogenet Evol 2015; 92:45-52. [DOI: 10.1016/j.ympev.2015.05.023] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 05/19/2015] [Accepted: 05/29/2015] [Indexed: 01/06/2023]
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Wölk A, Winterfeld G, Röser M. Genome evolution in a Mediterranean species complex: phylogeny and cytogenetics ofHelictotrichon(Poaceae) allopolyploids based on nuclear DNA sequences (rDNA, topoisomerase gene) and FISH. SYST BIODIVERS 2015. [DOI: 10.1080/14772000.2015.1023867] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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Zhang M, Rong Y, Lee MK, Zhang Y, Stelly DM, Zhang HB. Phylogenetic analysis of Gossypium L. using restriction fragment length polymorphism of repeated sequences. Mol Genet Genomics 2015; 290:1859-72. [PMID: 25877517 DOI: 10.1007/s00438-015-1039-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 03/27/2015] [Indexed: 10/23/2022]
Abstract
Cotton is the world's leading textile fiber crop and is also grown as a bioenergy and food crop. Knowledge of the phylogeny of closely related species and the genome origin and evolution of polyploid species is significant for advanced genomics research and breeding. We have reconstructed the phylogeny of the cotton genus, Gossypium L., and deciphered the genome origin and evolution of its five polyploid species by restriction fragment analysis of repeated sequences. Nuclear DNA of 84 accessions representing 35 species and all eight genomes of the genus were analyzed. The phylogenetic tree of the genus was reconstructed using the parsimony method on 1033 polymorphic repeated sequence restriction fragments. The genome origin of its polyploids was determined by calculating the diploid-polyploid restriction fragment correspondence (RFC). The tree is consistent with the morphological classification, genome designation and geographic distribution of the species at subgenus, section and subsection levels. Gossypium lobatum (D7) was unambiguously shown to have the highest RFC with the D-subgenomes of all five polyploids of the genus, while the common ancestor of Gossypium herbaceum (A1) and Gossypium arboreum (A2) likely contributed to the A-subgenomes of the polyploids. These results provide a comprehensive phylogenetic tree of the cotton genus and new insights into the genome origin and evolution of its polyploid species. The results also further demonstrate a simple, rapid and inexpensive method suitable for phylogenetic analysis of closely related species, especially congeneric species, and the inference of genome origin of polyploids that constitute over 70 % of flowering plants.
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Affiliation(s)
- Meiping Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA.,College of Life Science, Jilin Agricultural University, Changchun, 130118, Jilin, China
| | - Ying Rong
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Mi-Kyung Lee
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Yang Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - David M Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Hong-Bin Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA.
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Roy T, Cole LW, Chang TH, Lindqvist C. Untangling reticulate evolutionary relationships among New World and Hawaiian mints (Stachydeae, Lamiaceae). Mol Phylogenet Evol 2015; 89:46-62. [PMID: 25888973 DOI: 10.1016/j.ympev.2015.03.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 03/24/2015] [Accepted: 03/26/2015] [Indexed: 02/05/2023]
Abstract
The phenomenon of polyploidy and hybridization usually results in novel genetic combinations, leading to complex, reticulate evolution and incongruence among gene trees, which in turn may show different phylogenetic histories than the inherent species tree. The largest tribe within the subfamily Lamioideae (Lamiaceae), Stachydeae, which includes the globally distributed Stachys, and one of the largest Hawaiian angiosperm radiations, the endemic mints, is a widespread and taxonomically challenging lineage displaying a wide spectrum of morphological and chromosomal diversity. Previous molecular phylogenetic studies have showed that while the Hawaiian mints group with Mexican-South American Stachys based on chloroplast DNA sequence data, nuclear ribosomal DNA (nrDNA) sequences suggest that they are most closely related to temperate North American Stachys. Here, we have utilized five independently inherited, low-copy nuclear loci, and a variety of phylogenetic methods, including multi-locus coalescence-based tree reconstructions, to provide insight into the complex origins and evolutionary relationships between the New World Stachys and the Hawaiian mints. Our results demonstrate incongruence between individual gene trees, grouping the Hawaiian mints with both temperate North American and Meso-South American Stachys clades. However, our multi-locus coalescence tree is concurrent with previous nrDNA results placing them within the temperate North American Stachys clade. Our results point toward a possible allopolyploid hybrid origin of the Hawaiian mints arising from temperate North American and Meso-South American ancestors, as well as a reticulate origin for South American Stachys. As such, our study is another significant step toward further understanding the putative parentage and the potential influence of hybridization and incomplete lineage sorting in giving rise to this insular plant lineage, which following colonization underwent rapid morphological and ecological diversification.
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Affiliation(s)
- Tilottama Roy
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA.
| | - Logan W Cole
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA; Department of Biology, Indiana University, Bloomington, IN 47405, USA.
| | - Tien-Hao Chang
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA.
| | - Charlotte Lindqvist
- Department of Biological Sciences, University at Buffalo (SUNY), Buffalo, NY 14260, USA.
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Reis AC, Sousa SM, Vale AA, Pierre PMO, Franco AL, Campos JMS, Vieira RF, Viccini LF. Lippia alba (Verbenaceae): A new tropical autopolyploid complex? AMERICAN JOURNAL OF BOTANY 2014; 101:1002-1012. [PMID: 24920764 DOI: 10.3732/ajb.1400149] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
• Premise of the study: Tropical regions have high species diversity, and polyploidization is a major mechanism of speciation in plants. However, few cases of natural polyploidy have been reported in tropical regions. Lippia alba, is a tropical, aromatic shrub with a wide distribution, extensive morphological plasticity, and several chemotypes. The species has long been recognized as a diploid with 2n = 30 chromosomes. Recently, two variations in chromosome number (2n = 60; 2n = 12-60) have been reported, suggesting the occurrence of polyploidy within the species.• Methods: Flow cytometry was used to investigate the genome size in 106 accessions from 14 Brazilian States. Conventional and molecular cytogenetic techniques and pollen viability analysis were employed to characterize each chromosome number observed.• Key results: The DNA 1C-value varied from 1.17 to 3.45 pg, showing a large variation in genome size. Five distinct chromosome numbers were observed (2n = 30, 38, 45, 60, 90); three are cytogenetically described here for the first time. The 5S rDNA signals varied proportionally according to each chromosome number, but 45S rDNA sites did not. High rates of meiotic irregularity were observed, mainly in cytotypes with higher chromosome numbers.• Conclusions: The data provide new support for the occurrence of a polyploid series in Lippia alba. We provide a hypothesis for how this complex may have arisen. Other cryptic polyploid complexes may remain undiscovered in tropical regions.
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Affiliation(s)
- Aryane C Reis
- Universidade Federal de Juiz de Fora, Departamento de Biologia/Laboratório de Genética 36036-900, Juiz de Fora, MG, Brazil
| | - Saulo M Sousa
- Universidade Federal de Juiz de Fora, Departamento de Biologia/Laboratório de Genética 36036-900, Juiz de Fora, MG, Brazil
| | - Aline A Vale
- Universidade Federal de Juiz de Fora, Departamento de Biologia/Laboratório de Genética 36036-900, Juiz de Fora, MG, Brazil
| | - Patrícia M O Pierre
- Universidade Federal de Santa Catarina, Campus Universitário Curitibanos, Rodovia Ulisses Gaboardi-km 3 89520-000, Curitibanos, SC, Brazil
| | - Ana L Franco
- Universidade Federal de Juiz de Fora, Departamento de Biologia/Laboratório de Genética 36036-900, Juiz de Fora, MG, Brazil
| | - José Marcello S Campos
- Universidade Federal de Juiz de Fora, Departamento de Biologia/Laboratório de Genética 36036-900, Juiz de Fora, MG, Brazil
| | - Roberto F Vieira
- Embrapa Recursos Genéticos e Biotecnologia, CEP 70.770-900, Distrito Federal, Brasília, Brazil
| | - Lyderson F Viccini
- Universidade Federal de Juiz de Fora, Departamento de Biologia/Laboratório de Genética 36036-900, Juiz de Fora, MG, Brazil
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Galián JA, Rosato M, Rosselló JA. Partial Sequence Homogenization in the 5S Multigene Families May Generate Sequence Chimeras and Spurious Results in Phylogenetic Reconstructions. Syst Biol 2014; 63:219-30. [DOI: 10.1093/sysbio/syt101] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- José A. Galián
- Jardín Botánico, Universidad de Valencia, c/Quart 80, E-46008 Valencia, Spain; and 2Marimurtra Bot. Garden, Carl Faust Fdn., PO Box 112, E-17300 Blanes, Catalonia, Spain
| | - Marcela Rosato
- Jardín Botánico, Universidad de Valencia, c/Quart 80, E-46008 Valencia, Spain; and 2Marimurtra Bot. Garden, Carl Faust Fdn., PO Box 112, E-17300 Blanes, Catalonia, Spain
| | - Josep A. Rosselló
- Jardín Botánico, Universidad de Valencia, c/Quart 80, E-46008 Valencia, Spain; and 2Marimurtra Bot. Garden, Carl Faust Fdn., PO Box 112, E-17300 Blanes, Catalonia, Spain
- Jardín Botánico, Universidad de Valencia, c/Quart 80, E-46008 Valencia, Spain; and 2Marimurtra Bot. Garden, Carl Faust Fdn., PO Box 112, E-17300 Blanes, Catalonia, Spain
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29
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Roy T, Chang TH, Lan T, Lindqvist C. Phylogeny and biogeography of New World Stachydeae (Lamiaceae) with emphasis on the origin and diversification of Hawaiian and South American taxa. Mol Phylogenet Evol 2013; 69:218-38. [DOI: 10.1016/j.ympev.2013.05.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/25/2013] [Accepted: 05/30/2013] [Indexed: 12/15/2022]
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Systematic application of DNA fiber-FISH technique in cotton. PLoS One 2013; 8:e75674. [PMID: 24086609 PMCID: PMC3785504 DOI: 10.1371/journal.pone.0075674] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 08/09/2013] [Indexed: 01/16/2023] Open
Abstract
Fluorescence in situ hybridization on extended DNA (fiber-FISH) is a powerful tool in high-resolution physical mapping. To introduce this technique into cotton, we developed the technique and tested it by deliberately mapping of telomere and 5S rDNA. Results showed that telomere-length ranged from 0.80 kb to 37.86 kb in three species, G. hirsutum, G. herbaceum and G. arboreum. However, most of the telomeres (>91.0%) were below 10 kb. The length of 5S rDNA was revealed as 964 kb in G. herbaceum whereas, in G. arboreum, it was approximately three times longer (3.1 Mb). A fiber-FISH based immunofluorescence method was also described to assay the DNA methylation. Using this technique, we revealed that both telomere and 5S rDNA were methylated at different levels. In addition, we developed a BAC molecule-based fiber-FISH technique. Using this technique, we can precisely map BAC clones on each other and evaluated the size and location of overlapped regions. The development and application of fiber-FISH technique will facilitate high-resolution physical mapping and further directed sequencing projects for cotton.
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31
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Waminal NE, Ryu KB, Park BR, Kim HH. Phylogeny of Cucurbitaceae species in Korea based on 5S rDNA non-transcribed spacer. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0141-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Wong KL, But PPH, Shaw PC. Evaluation of seven DNA barcodes for differentiating closely related medicinal Gentiana species and their adulterants. Chin Med 2013; 8:16. [PMID: 23962024 PMCID: PMC3766668 DOI: 10.1186/1749-8546-8-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 08/18/2013] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Species identification of living organisms by standard DNA sequences has been well-accepted. Consortium for the Barcode of Life (CBOL) recommends chloroplast regions rbcL and matK as the DNA barcodes for the land plants. This study aims to evaluate the feasibility and limitations of rbcL, matK, and 5 other commonly used regions as the DNA barcodes for the medicinal Gentiana and their adulterants, Gentiana. rhodantha and Podophyllum hexandrum. METHODS The species differentiation power of rbcL, matK, nuclear internal transcribed spacer (ITS) and 5S rRNA intergenic spacer, and chloroplast trnH-psbA, trnL-F and rpl36-rps8 intergenic spacers were tested in different medicinal Gentiana, including Gentiana scabra, Gentiana triflora, Gentiana manshurica and Gentiana rigescens, from common adulterants such as Gentiana rhodantha and Podophyllum hexandrum (a toxic herb producing podophyllotoxin). RESULTS All seven tested loci could be used to differentiate medicinal Gentiana species from their adulterants, and to distinguish Guanlongdan from Jianlongdan. In terms of general differentiation powers, rbcL and matK had no significant advantages over the other five loci. Only the 5S rRNA and trnL-F intergenic spacers were able to discriminate the closely related species G. triflora, G. scabra and G. manshurica. CONCLUSION The DNA barcodes rbcL and matK are useful in differentiation of closely related medicinal species of Gentiana, but had no significant advantages over the other five tested loci.
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Affiliation(s)
- Ka-Lok Wong
- State Key Laboratory of Phytochemistry and Plant Resources in West China (CUHK), Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Paul Pui-Hay But
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Pang-Chui Shaw
- State Key Laboratory of Phytochemistry and Plant Resources in West China (CUHK), Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong, China
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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Wu Q, Liu F, Li S, Song G, Wang C, Zhang X, Wang Y, Stelly D, Wang K. Uniqueness of the Gossypium mustelinum genome revealed by GISH and 45S rDNA FISH. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:654-62. [PMID: 23758934 PMCID: PMC3810724 DOI: 10.1111/jipb.12084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 05/24/2013] [Indexed: 05/23/2023]
Abstract
Gossypium mustelinum ((AD)4 ) is one of five disomic species in Gossypium. Three 45S ribosomal DNA (rDNA) loci were detected in (AD)4 with 45S rDNA as probe, and three pairs of brighter signals were detected with genomic DNA (gDNA) of Gossypium D genome species as probes. The size and the location of these brighter signals were the same as those detected with 45S rDNA as probe, and were named GISH-NOR. One of them was super-major, which accounted for the fact that about one-half of its chromosome at metaphase was located at chromosome 3, and other two were minor and located at chromosomes 5 and 9, respectively. All GISH-NORs were located in A sub-genome chromosomes, separate from the other four allopolyploid cotton species. GISH-NOR were detected with D genome species as probe, but not A. The greatly abnormal sizes and sites of (AD)4 NORs or GISH-NORs indicate a possible mechanism for 45S rDNA diversification following (AD)4 speciation. Comparisons of GISH intensities and GISH-NOR production with gDNA probes between A and D genomes show that the better relationship of (AD)4 is with A genome. The shortest two chromosomes of A sub-genome of G. mustelinum were shorter than the longest chromosome of D sub-genome chromosomes. Therefore, the longest 13 chromosomes of tetraploid cotton being classified as A sub-genome, while the shorter 13 chromosomes being classified as D sub-genome in traditional cytogenetic and karyotype analyses may not be entirely correct.
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Affiliation(s)
- Qiong Wu
- Cotton Research Institute, the Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton BiologyAnyang, 455000, China
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural SciencesHaikou, 570102, China
| | - Fang Liu
- Cotton Research Institute, the Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton BiologyAnyang, 455000, China
| | - Shaohui Li
- Cotton Research Institute, the Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton BiologyAnyang, 455000, China
| | - Guoli Song
- Cotton Research Institute, the Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton BiologyAnyang, 455000, China
| | - Chunying Wang
- Cotton Research Institute, the Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton BiologyAnyang, 455000, China
| | - Xiangdi Zhang
- Cotton Research Institute, the Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton BiologyAnyang, 455000, China
| | - Yuhong Wang
- Cotton Research Institute, the Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton BiologyAnyang, 455000, China
| | - David Stelly
- Department of Soil and Crop Sciences, Texas A&M UniversityCollege Station, Texas, 77843-2474, USA
| | - Kunbo Wang
- Cotton Research Institute, the Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton BiologyAnyang, 455000, China
- * Corresponding author, Tel: + 86 372 256 2204; Fax: +86 372 252 5377; E-mail:
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Weiss-Schneeweiss H, Emadzade K, Jang TS, Schneeweiss G. Evolutionary consequences, constraints and potential of polyploidy in plants. Cytogenet Genome Res 2013; 140:137-50. [PMID: 23796571 PMCID: PMC3859924 DOI: 10.1159/000351727] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Polyploidy, the possession of more than 2 complete genomes, is a major force in plant evolution known to affect the genetic and genomic constitution and the phenotype of an organism, which will have consequences for its ecology and geography as well as for lineage diversification and speciation. In this review, we discuss phylogenetic patterns in the incidence of polyploidy including possible underlying causes, the role of polyploidy for diversification, the effects of polyploidy on geographical and ecological patterns, and putative underlying mechanisms as well as chromosome evolution and evolution of repetitive DNA following polyploidization. Spurred by technological advances, a lot has been learned about these aspects both in model and increasingly also in nonmodel species. Despite this enormous progress, long-standing questions about polyploidy still cannot be unambiguously answered, due to frequently idiosyncratic outcomes and insufficient integration of different organizational levels (from genes to ecology), but likely this will change in the near future. See also the sister article focusing on animals by Choleva and Janko in this themed issue.
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Affiliation(s)
- H. Weiss-Schneeweiss
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - K. Emadzade
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - T.-S. Jang
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
| | - G.M. Schneeweiss
- Department of Systematic and Evolutionary Botany University of Vienna, Rennweg 14 AT–1030 Vienna (Austria)
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Mahelka V, Kopecký D, Baum BR. Contrasting Patterns of Evolution of 45S and 5S rDNA Families Uncover New Aspects in the Genome Constitution of the Agronomically Important Grass Thinopyrum intermedium (Triticeae). Mol Biol Evol 2013; 30:2065-86. [DOI: 10.1093/molbev/mst106] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Kushwaha B, Nagpure NS. Characterization and physical mapping of 18S and 5S ribosomal genes in Indian major carps (Pisces, Cyprinidae). Micron 2013; 49:40-5. [PMID: 23587674 DOI: 10.1016/j.micron.2013.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 03/07/2013] [Accepted: 03/10/2013] [Indexed: 11/17/2022]
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Falistocco E, Marconi G. Cytogenetic characterization by in situ hybridization techniques and molecular analysis of 5S rRNA genes of the European hazelnut (Corylus avellana). Genome 2013; 56:155-9. [PMID: 23659699 DOI: 10.1139/gen-2013-0045] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The European hazelnut (Corylus avellana L.) is widespread in Europe, where it has been cultivated for centuries. Despite progress in genetics, most of the cytogenetic aspects of this species have been overlooked. The aim of this study was to fill in this gap and obtain basic information on the chromosome structure of this species. Karyomorphological analysis confirmed the chromosome number 2n = 22 and showed that, despite their apparent uniformity, the chromosomes could be separated into three groups of different size: large (L), medium (M), and small (S). As a first step towards the physical mapping of the hazelnut chromosomes, we applied FISH to localize the position of rRNA genes (rDNA). The sites of 45S and 5S rDNA enabled us to identify two chromosome pairs belonging, respectively, to the L and S groups. The self-GISH procedure revealed that repetitive DNA is concentrated in the pericentromeric regions of the chromosomes, as with other species with rather small genomes. The analysis of 5S rDNA repeats offered additional information on the hazelnut genome by obtaining the whole sequence of the transcribed region so far unpublished. The overall results constitute a substantial advance in hazelnut cytogenetics. Further investigation of other species of Corylus could be an effective approach to understanding the phylogenesis of the genus and resolving taxonomic problems.
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Affiliation(s)
- E Falistocco
- Department of Applied Biology, University of Perugia, Borgo XX Giugno, 06100 Perugia, Italy.
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Naidoo K, Steenkamp ET, Coetzee MPA, Wingfield MJ, Wingfield BD. Concerted evolution in the ribosomal RNA cistron. PLoS One 2013; 8:e59355. [PMID: 23555022 PMCID: PMC3595265 DOI: 10.1371/journal.pone.0059355] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 02/13/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Gene conversion is the mechanism proposed to be responsible for the homogenization of multigene families such as the nuclear ribosomal gene clusters. This concerted evolutionary process prevents individual genes in gene clusters from accumulating mutations. The mechanism responsible for concerted evolution is not well understood but recombination during meiosis has been hypothesized to play a significant role in this homogenization. In this study we tested the hypothesis of unequal crossing over playing a significant role in gene conversion events within the ribosomal RNA cistron during meiosis, mitosis or both life stages in the fungal tree pathogen Ceratocystis manginecans. METHODS Ceratocystis manginecans, a haploid ascomycete, reproduces homothallically and was found to have two distinct sequences within the internally transcribed spacer (ITS) region of the ribosomal RNA cistron. The different ITS types were scored using PCR-RFLP assays and chi-square analyses to determine the level of significance of the changes in the ratios of the ITS types. RESULTS The relative ratios of the two ITS sequence types changed when the fungal isolates were cultured vegetatively or allowed to produced sexual structures and spores. These active changes were shown to occur more frequently during meiosis than mitosis. CONCLUSION The evidence presented provides concrete support for homogenization in the rRNA gene clusters found in this fungus and that the most reasonable explanation for this process is unequal crossing over.
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Affiliation(s)
- Kershney Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Faculty of Natural and Agricultural Sciences, Pretoria, South Africa
| | - Emma T. Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Faculty of Natural and Agricultural Sciences, Pretoria, South Africa
| | - Martin P. A. Coetzee
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Faculty of Natural and Agricultural Sciences, Pretoria, South Africa
| | - Michael J. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Faculty of Natural and Agricultural Sciences, Pretoria, South Africa
| | - Brenda D. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Faculty of Natural and Agricultural Sciences, Pretoria, South Africa
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Seo JH, Bae HG, Park DH, Kim BS, Lee JW, Lee JI, Kim DH, Lee SW, Seo BB. Sequence polymorphisms in ribosomal RNA genes and variations in chromosomal loci of Oenothera odorata and O. laciniata. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0084-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Dimarco E, Cascone E, Bellavia D, Caradonna F. Functional variants of 5S rRNA in the ribosomes of common sea urchin Paracentrotus lividus. Gene 2012; 508:21-5. [PMID: 22967708 DOI: 10.1016/j.gene.2012.07.067] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 07/30/2012] [Indexed: 11/28/2022]
Abstract
We have previously reported a molecular and cytogenetic characterization of three different 5S rDNA clusters in the sea urchin Paracentrotus lividus; this study, performed at DNA level only, lends itself as starting point to verify that these clusters could contain transcribed genes, then, to demonstrate the presence of heterogeneity at functional RNA level, also. In the present work we report in P. lividus ribosomes the existence of several transcribed variants of the 5S rRNA and we associate all transcribed variants to the cluster to which belong. Our finding is the first demonstration of the presence of high heterogeneity in functional 5S rRNA molecules in animal ribosomes, a feature that had been considered a peculiarity of some plants.
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Affiliation(s)
- Eufrosina Dimarco
- Dipartimento di Scienze e Tecnologie Molecolari e Biomolecolari (STEMBIO), Sezione di Biologia Cellulare, Università degli Studi di Palermo, V.le delle Scienze—90128 Palermo, Italy
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Types, levels and patterns of low-copy DNA sequence divergence, and phylogenetic implications, for Gossypium genome types. Heredity (Edinb) 2012; 108:500-6. [PMID: 22511177 DOI: 10.1038/hdy.2011.111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
To explore types, levels and patterns of genetic divergence among diploid Gossypium (cotton) genomes, 780 cDNA, genomic DNA and simple sequence repeat (SSR) loci were re-sequenced in Gossypium herbaceum (A1 genome), G. arboreum (A2), G. raimondii (D5), G. trilobum (D8), G. sturtianum (C1) and an outgroup, Gossypioides kirkii. Divergence among these genomes ranged from 7.32 polymorphic base pairs per 100 between G. kirkii and G. herbaceum (A1) to only 1.44 between G. herbaceum (A1) and G. arboreum (A2). SSR loci are least conserved with 12.71 polymorphic base pairs and 3.77 polymorphic sites per 100 base pairs, whereas expressed sequence tags are most conserved with 3.96 polymorphic base pairs and 2.06 sites. SSR loci also exhibit the highest percentage of 'extended polymorphisms' (spanning multiple consecutive nucleotides). The A genome lineage was particularly rapidly evolving, with the D genome also showing accelerated evolution relative to the C genome. Unexpected asymmetry in mutation rates was found, with much more transition than transversion mutation in the D genome after its divergence from a common ancestor shared with the A genome. This large quantity of orthologous DNA sequence strongly supports a phylogeny in which A-C divergence is more recent than A-D divergence, a subject that is of much importance in view of A-D polyploid formation being key to the evolution of the most productive and finest-quality cottons. Loci that are monomorphic within A or D genome types, but polymorphic between genome types, may be of practical importance for identifying locus-specific DNA markers in tetraploid cottons including leading cultivars.
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Mlinarec J, Satović Z, Mihelj D, Malenica N, Besendorfer V. Cytogenetic and phylogenetic studies of diploid and polyploid members of tribe Anemoninae (Ranunculaceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2012; 14:525-36. [PMID: 22188120 DOI: 10.1111/j.1438-8677.2011.00519.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The ancestry, phylogenetic differentiation and systematic classification of the worldwide-distributed genus Anemone have been debated for many years. In this paper 11 Anemone, three Pulsatilla species and Hepatica nobilis were subjected to detailed karyotype analysis with the aim of obtaining new cytogenetic data that will contribute to karyotype evolutionary studies of the tribe Anemoninae. The results are interpreted in a phylogenetic context, established from the intergenic nontranscribed spacer (NTS) of 5S rDNA and internal transcribed spacer (ITS) of 35S rDNA. One to three 35S and one to three 5S rDNA loci are present in diploid and polyploid taxa. The 35S rDNA loci are located terminally on the short arm of acrocentric chromosomes, while for 5S rDNA there is no preferential chromosomal position as it exhibits terminal, subterminal, interstitial or pericentromeric positions, and is located either on acrocentric or metacentric chromosomes. The karyotype of hexaploid A. baldensis (2n = 6x = 48) is presented for the first time, and A. sylvestris is proposed as one of its putative parental species. Chromosome fusion/translocation is proposed as the key mechanism involved in reduction of the basic chromosome number from 8 in the Anemone subgenus to 7 in the Anemonidium subgenus. The cytogenetic data obtained are mainly supported by ITS and NTS phylogeny. Diversification of the genus Anemone was accompanied by a large reduction of heterochromatin, from the Mediterranean anemones that have large amounts of heterochromatin to the New World anemones without any detectable heterochromatic blocks.
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Affiliation(s)
- J Mlinarec
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia.
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Merlo MA, Pacchiarini T, Portela-Bens S, Cross I, Manchado M, Rebordinos L. Genetic characterization of Plectorhinchus mediterraneus yields important clues about genome organization and evolution of multigene families. BMC Genet 2012; 13:33. [PMID: 22545758 PMCID: PMC3464664 DOI: 10.1186/1471-2156-13-33] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 04/30/2012] [Indexed: 12/17/2022] Open
Abstract
Background Molecular and cytogenetic markers are of great use for to fish characterization, identification, phylogenetics and evolution. Multigene families have proven to be good markers for a better understanding of the variability, organization and evolution of fish species. Three different tandemly-repeated gene families (45S rDNA, 5S rDNA and U2 snDNA) have been studied in Plectorhinchus mediterraneus (Teleostei: Haemulidae), at both molecular and cytogenetic level, to elucidate the taxonomy and evolution of these multigene families, as well as for comparative purposes with other species of the family. Results Four different types of 5S rDNA were obtained; two of them showed a high homology with that of Raja asterias, and the putative implication of a horizontal transfer event and its consequences for the organization and evolution of the 5S rDNA have been discussed. The other two types do not resemble any other species, but in one of them a putative tRNA-derived SINE was observed for the first time, which could have implications in the evolution of the 5S rDNA. The ITS-1 sequence was more related to a species of another different genus than to that of the same genus, therefore a revision of the Hamulidae family systematic has been proposed. In the analysis of the U2 snDNA, we were able to corroborate that U2 snDNA and U5 snDNA were linked in the same tandem array, and this has interest for tracing evolutionary lines. The karyotype of the species was composed of 2n = 48 acrocentric chromosomes, and each of the three multigene families were located in different chromosome pairs, thus providing three different chromosomal markers. Conclusions Novel data can be extracted from the results: a putative event of horizontal transfer, a possible tRNA-derived SINE linked to one of the four 5S rDNA types characterized, and a linkage between U2 and U5 snDNA. In addition, a revision of the taxonomy of the Haemulidae family has been suggested, and three cytogenetic markers have been obtained. Some of these results have not been described before in any other fish species. New clues about the genome organization and evolution of the multigene families are offered in this study.
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Affiliation(s)
- Manuel A Merlo
- Laboratorio de Genética, Universidad de Cádiz, Polígono Río San Pedro 11510, Puerto Real, Cádiz, Spain
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Molecular evolution and phylogenetic analysis of genes related to cotton fibers development from wild and domesticated cotton species in Gossypium. Mol Phylogenet Evol 2012; 63:589-97. [PMID: 22381639 DOI: 10.1016/j.ympev.2012.01.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 01/30/2012] [Accepted: 01/31/2012] [Indexed: 12/23/2022]
Abstract
The domestication of both diploid and tetraploid cotton species was carried out for fiber utilization. To understand the origin and domestication of fibers, 18 genes related to fiber development were individually cloned and sequenced from 22 different cotton species. Their structures, phylogenetic relationship and molecular evolution were further studied. In the orthologous and homeologous loci of the 18 genes, the sequence and structure of 72.22% were conserved and 27.78% were diverse. Tree topologies constructed based on the combined sequences showed that all 13 D-genome species were congruent with Fryxell's subsection taxonomy, the A- and D-subgenomes independently evolved in the allopolyploid after polyploid formation, and Gossypium raimondii had the closest relationship with all allotetraploids of D-subgenomes. The molecular evolutionary rates revealed approximately equivalent rates among different D-genome species, and purifying selection acted on all genes in the wild D-genome species. Among orthologs and homeologs, the D-subgenomes had higher evolutionary rates than the A-subgenomes in tetraploid cotton species, and the cultivars had higher evolutionary rates than either the semi-domesticated or wild species. Our study revealed that human domestication altered the molecular evolutionary pattern of genes related to fiber development, and Gossypium hirsutum endured greater selective pressures than Gossypium barbadense during the domestication process.
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Lan T, Albert VA. Dynamic distribution patterns of ribosomal DNA and chromosomal evolution in Paphiopedilum, a lady's slipper orchid. BMC PLANT BIOLOGY 2011; 11:126. [PMID: 21910890 PMCID: PMC3184063 DOI: 10.1186/1471-2229-11-126] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 09/12/2011] [Indexed: 05/07/2023]
Abstract
Background Paphiopedilum is a horticulturally and ecologically important genus of ca. 80 species of lady's slipper orchids native to Southeast Asia. These plants have long been of interest regarding their chromosomal evolution, which involves a progressive aneuploid series based on either fission or fusion of centromeres. Chromosome number is positively correlated with genome size, so rearrangement processes must include either insertion or deletion of DNA segments. We have conducted Fluorescence In Situ Hybridization (FISH) studies using 5S and 25S ribosomal DNA (rDNA) probes to survey for rearrangements, duplications, and phylogenetically-correlated variation within Paphiopedilum. We further studied sequence variation of the non-transcribed spacers of 5S rDNA (5S-NTS) to examine their complex duplication history, including the possibility that concerted evolutionary forces may homogenize diversity. Results 5S and 25S rDNA loci among Paphiopedilum species, representing all key phylogenetic lineages, exhibit a considerable diversity that correlates well with recognized evolutionary groups. 25S rDNA signals range from 2 (representing 1 locus) to 9, the latter representing hemizygosity. 5S loci display extensive structural variation, and show from 2 specific signals to many, both major and minor and highly dispersed. The dispersed signals mainly occur at centromeric and subtelomeric positions, which are hotspots for chromosomal breakpoints. Phylogenetic analysis of cloned 5S rDNA non-transcribed spacer (5S-NTS) sequences showed evidence for both ancient and recent post-speciation duplication events, as well as interlocus and intralocus diversity. Conclusions Paphiopedilum species display many chromosomal rearrangements - for example, duplications, translocations, and inversions - but only weak concerted evolutionary forces among highly duplicated 5S arrays, which suggests that double-strand break repair processes are dynamic and ongoing. These results make the genus a model system for the study of complex chromosomal evolution in plants.
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Affiliation(s)
- Tianying Lan
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
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Sultana S, Bang JW, Choi HW. Organization of the 5S rRNA gene units in Korean Lilium species. Genes Genomics 2011. [DOI: 10.1007/s13258-010-0131-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Straub SCK, Fishbein M, Livshultz T, Foster Z, Parks M, Weitemier K, Cronn RC, Liston A. Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing. BMC Genomics 2011; 12:211. [PMID: 21542930 PMCID: PMC3116503 DOI: 10.1186/1471-2164-12-211] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Accepted: 05/04/2011] [Indexed: 01/05/2023] Open
Abstract
Background Milkweeds (Asclepias L.) have been extensively investigated in diverse areas of evolutionary biology and ecology; however, there are few genetic resources available to facilitate and compliment these studies. This study explored how low coverage genome sequencing of the common milkweed (Asclepias syriaca L.) could be useful in characterizing the genome of a plant without prior genomic information and for development of genomic resources as a step toward further developing A. syriaca as a model in ecology and evolution. Results A 0.5× genome of A. syriaca was produced using Illumina sequencing. A virtually complete chloroplast genome of 158,598 bp was assembled, revealing few repeats and loss of three genes: accD, clpP, and ycf1. A nearly complete rDNA cistron (18S-5.8S-26S; 7,541 bp) and 5S rDNA (120 bp) sequence were obtained. Assessment of polymorphism revealed that the rDNA cistron and 5S rDNA had 0.3% and 26.7% polymorphic sites, respectively. A partial mitochondrial genome sequence (130,764 bp), with identical gene content to tobacco, was also assembled. An initial characterization of repeat content indicated that Ty1/copia-like retroelements are the most common repeat type in the milkweed genome. At least one A. syriaca microread hit 88% of Catharanthus roseus (Apocynaceae) unigenes (median coverage of 0.29×) and 66% of single copy orthologs (COSII) in asterids (median coverage of 0.14×). From this partial characterization of the A. syriaca genome, markers for population genetics (microsatellites) and phylogenetics (low-copy nuclear genes) studies were developed. Conclusions The results highlight the promise of next generation sequencing for development of genomic resources for any organism. Low coverage genome sequencing allows characterization of the high copy fraction of the genome and exploration of the low copy fraction of the genome, which facilitate the development of molecular tools for further study of a target species and its relatives. This study represents a first step in the development of a community resource for further study of plant-insect co-evolution, anti-herbivore defense, floral developmental genetics, reproductive biology, chemical evolution, population genetics, and comparative genomics using milkweeds, and A. syriaca in particular, as ecological and evolutionary models.
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Affiliation(s)
- Shannon C K Straub
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA.
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Fukushima K, Imamura K, Nagano K, Hoshi Y. Contrasting patterns of the 5S and 45S rDNA evolutions in the Byblis liniflora complex (Byblidaceae). JOURNAL OF PLANT RESEARCH 2011; 124:231-44. [PMID: 20623155 PMCID: PMC3040357 DOI: 10.1007/s10265-010-0366-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 06/11/2010] [Indexed: 05/07/2023]
Abstract
To clarify the evolutionary dynamics of ribosomal RNA genes (rDNAs) in the Byblis liniflora complex (Byblidaceae), we investigated the 5S and 45S rDNA genes through (1) chromosomal physical mapping by fluorescence in situ hybridization (FISH) and (2) phylogenetic analyses using the nontranscribed spacer of 5S rDNA (5S-NTS) and the internal transcribed spacer of 45S rDNA (ITS). In addition, we performed phylogenetic analyses based on rbcL and trnK intron. The complex was divided into 2 clades: B. aquatica-B. filifolia and B. guehoi-B. liniflora-B. rorida. Although members of the complex had conservative symmetric karyotypes, they were clearly differentiated on chromosomal rDNA distribution patterns. The sequence data indicated that ITS was almost homogeneous in all taxa in which two or four 45S rDNA arrays were frequently found at distal regions of chromosomes in the somatic karyotype. ITS homogenization could have been prompted by relatively distal 45S rDNA positions. In contrast, 2-12 5S rDNA arrays were mapped onto proximal/interstitial regions of chromosomes, and some paralogous 5S-NTS were found in the genomes harboring 4 or more arrays. 5S-NTS sequence type-specific FISH analysis showed sequence heterogeneity within and between some 5S rDNA arrays. Interlocus homogenization may have been hampered by their proximal location on chromosomes. Chromosomal location may have affected the contrasting evolutionary dynamics of rDNAs in the B. liniflora complex.
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Affiliation(s)
- Kenji Fukushima
- Department of Basic Biology, The Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193 Japan
- Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki, Aichi 444-8585 Japan
| | - Kaori Imamura
- Department of Plant Science, School of Agriculture, Tokai University, Kawayou, Minamiaso-mura, Aso-gun, Kumamoto, 869-1404 Japan
- Japan Software Management Co. Ltd., 5-32 KinKou-cho, Kanagawa-ku, Yokohama, Kanagawa 221-0056 Japan
| | - Katsuya Nagano
- Department of Plant Science, School of Agriculture, Tokai University, Kawayou, Minamiaso-mura, Aso-gun, Kumamoto, 869-1404 Japan
| | - Yoshikazu Hoshi
- Department of Plant Science, School of Agriculture, Tokai University, Kawayou, Minamiaso-mura, Aso-gun, Kumamoto, 869-1404 Japan
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Mani I, Kumar R, Singh M, Nagpure NS, Kushwaha B, Srivastava PK, Rao DSK, Lakra WS. Nucleotide variation and physical mapping of ribosomal genes using FISH in genus Tor (Pisces, Cyprinidae). Mol Biol Rep 2010; 38:2637-47. [PMID: 21104144 DOI: 10.1007/s11033-010-0405-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2010] [Accepted: 11/08/2010] [Indexed: 10/18/2022]
Abstract
Molecular cytogenetic studies were carried out for localization of 18S and 5S ribosomal DNAs on chromosomes of three cyprinid fish species viz., T. khudree, T. mussullah and T. mosal mahanadicus using two color fluorescence in situ hybridization (FISH). All the species typically possessed 100 diploid chromosomes with minor variation in karyo-morphology. The 18S rDNA signals were observed on two pair of chromosomes in T. khudree and T. mussullah, and three pairs in T. mosal mahanadicus. The location of 18S signals also showed affinity to silver nitrate and chromomycin A3 staining. Similarly, variation in localization of 5S rDNA among the three species has been detected with the presence of FISH signals on one pair of chromosome in T. khudree and T. mussullah, and on two pairs in T. mosal mahanadicus. These molecular markers could be used as species specific markers for taxonomic identification and can further add in understanding the dynamics of genome organization and karyotypic evolution of these species. The 18S rDNA region was sequenced that generated 1811, 1810 and 1776 bp long 18S sequence in T. khudree, T. mussullah and T. mosal mahanadicus, respectively. The 18S rDNA sequence showed 95-98% identity among the subject species. Similarly, 5S sequencing generated 203 bp long fragments in these species with 100% identity in coding and 9.63% variability in non-transcribed spacer regions. The nucleotide sequence variations could be used for understanding the genetic diversity and will add new informative characters in comparative genomics. These results, in general, would enhance the value and interpretation of ecological assessment data for conservation of Tor species.
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Affiliation(s)
- Indra Mani
- National Bureau of Fish Genetic Resources, Canal Ring Road, P.O. Dilkusha, Lucknow, 226 002, U.P., India
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Baum BR, Feldman M. Elimination of 5S DNA unit classes in newly formed allopolyploids of the genera Aegilops and Triticum. Genome 2010; 53:430-8. [PMID: 20555432 DOI: 10.1139/g10-017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two classes of 5S DNA units, namely the short (containing units of 410 bp) and the long (containing units of 500 bp), are recognized in species of the wheat (the genera Aegilops and Triticum) group. While every diploid species of this group contains 2 unit classes, the short and the long, every allopolyploid species contains a smaller number of unit classes than the sum of the unit classes of its parental species. The aim of this study was to determine whether the reduction in these unit classes is due to the process of allopolyploidization, that is, interspecific or intergeneric hybridization followed by chromosome doubling, and whether it occurs during or soon after the formation of the allopolyploids. To study this, the number and types of unit classes were determined in several newly formed allotetraploids, allohexaploids, and an allooctoploid of Aegilops and Triticum. It was found that elimination of unit classes of 5S DNA occurred soon (in the first 3 generations) after the formation of the allopolyploids. This elimination was reproducible, that is, the same unit classes were eliminated in natural and synthetic allopolyploids having the same genomic combinations. No further elimination occurred in the unit classes of the 5S DNA during the life of the allopolyploid. The genetic and evolutionary significance of this elimination as well as the difference in response to allopolyploidization of 5S DNA and rDNA are discussed.
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Affiliation(s)
- B R Baum
- Agriculture and Agri-Food Canada, Neatby Building, Ottawa, ON, Canada.
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