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Wang W, Zhang X, Garcia S, Leitch AR, Kovařík A. Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between? Heredity (Edinb) 2023; 131:179-188. [PMID: 37402824 PMCID: PMC10462631 DOI: 10.1038/s41437-023-00634-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
The classical model of concerted evolution states that hundreds to thousands of ribosomal DNA (rDNA) units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected given mutation frequencies and gene redundancy. While the universality of this over 50-year-old model has been confirmed in a range of organisms, advanced high throughput sequencing techniques have also revealed that rDNA homogenization in many organisms is partial and, in rare cases, even apparently failing. The potential underpinning processes leading to unexpected intragenomic variation have been discussed in a number of studies, but a comprehensive understanding remains to be determined. In this work, we summarize information on variation or polymorphisms in rDNAs across a wide range of taxa amongst animals, fungi, plants, and protists. We discuss the definition and description of concerted evolution and describe whether incomplete concerted evolution of rDNAs predominantly affects coding or non-coding regions of rDNA units and if it leads to the formation of pseudogenes or not. We also discuss the factors contributing to rDNA variation, such as interspecific hybridization, meiotic cycles, rDNA expression status, genome size, and the activity of effector genes involved in genetic recombination, epigenetic modifications, and DNA editing. Finally, we argue that a combination of approaches is needed to target genetic and epigenetic phenomena influencing incomplete concerted evolution, to give a comprehensive understanding of the evolution and functional consequences of intragenomic variation in rDNA.
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Affiliation(s)
- Wencai Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Xianzhi Zhang
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Sònia Garcia
- Institut Botànic de Barcelona, IBB (CSIC - Ajuntament de Barcelona), Barcelona, Spain
| | - Andrew R Leitch
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61200, Czech Republic.
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Belyakov EA, Mikhaylova YV, Machs EM, Zhurbenko PM, Rodionov AV. Hybridization and diversity of aquatic macrophyte Sparganium L. (Typhaceae) as revealed by high-throughput nrDNA sequencing. Sci Rep 2022; 12:21610. [PMID: 36517537 PMCID: PMC9750990 DOI: 10.1038/s41598-022-25954-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
Sparganium is an emergent aquatic macrophyte widely spread in temperate and subtropical zones. Taxa of this genus feature high phenotypic plasticity and can produce interspecific hybrids. By means of high-throughput sequencing of the internal transcribed spacer (ITS1) of 35S rDNA, the status of 15 Eurasian Sparganium species and subspecies was clarified and the role of hybridization events in the recent evolution of the genus was investigated. It has been shown that a number of species such as S. angustifolium, S. fallax and S. subglobosum have homogenized rDNA represented by one major ribotype. The rDNA of other taxa is represented by two or more major ribotypes. Species with high rDNA heterogeneity are apparently of hybrid origin. Based on the differences in rDNA patterns, intraspecific diversity was identified in S. probatovae and S. emersum. Thus, we have concluded that Sparganium has extensive interspecific hybridization at the subgenus level, and there may also be occasional hybridization between species from different subgenera.
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Affiliation(s)
- Evgeny A. Belyakov
- grid.464570.40000 0001 1092 3616Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Yaroslavl Region, Nekouz District, 109, Borok, Russia 152742 ,grid.446199.70000 0000 8543 3323Cherepovets State University, Lunacharsky Ave., 5, Cherepovets, Russia 162600
| | - Yulia V. Mikhaylova
- grid.465298.4Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova St., 2, St. Petersburg, Russia 199376
| | - Eduard M. Machs
- grid.465298.4Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova St., 2, St. Petersburg, Russia 199376
| | - Peter M. Zhurbenko
- grid.465298.4Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova St., 2, St. Petersburg, Russia 199376 ,grid.15447.330000 0001 2289 6897St. Petersburg State University, Universitetskaya Embankment, 7-9, St. Petersburg, Russia 199034
| | - Aleksandr V. Rodionov
- grid.465298.4Komarov Botanical Institute, Russian Academy of Sciences, Prof. Popova St., 2, St. Petersburg, Russia 199376 ,grid.15447.330000 0001 2289 6897St. Petersburg State University, Universitetskaya Embankment, 7-9, St. Petersburg, Russia 199034
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Ansari HA, Ellison N, Stewart AV, Williams WM. Distribution patterns of rDNA loci in the Schedonorus- Lolium complex (Poaceae). COMPARATIVE CYTOGENETICS 2022; 16:39-54. [PMID: 35437460 PMCID: PMC8971122 DOI: 10.3897/compcytogen.v16.i1.79056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
The Schedonorus-Lolium complex of the subtribe Loliinae (Poaceae) includes several economically important forage and turf grasses. This complex encompasses Lolium Linnaeus, 1753, Festuca Linnaeus, 1753 subgenus Schedonorus (P. Beauvois, 1824) Petermann, 1849 and Micropyropsis Romero Zarco et Cabezudo, 1983. New FISH results of 5S and 18S-26S rDNA sequences are presented for three species and the results are interpreted in a review of distribution patterns of 5S and 18S-26S rDNA sequences among other species in the complex. Micropyropsistuberosa Romero Zarco et Cabezudo, 1983 (2n = 2x = 14) displayed a distribution pattern of rDNA sequences identical to that of F.pratensis Hudson, 1762, supporting a close phylogenetic relationship at the bottom of the phylogenetic tree. "Loliummultiflorum" Lamarck, 1779 accessions sourced from Morocco showed a different pattern from European L.multiflorum and could be a unique and previously uncharacterised taxon. North African Festucasimensis Hochstetter ex A. Richard, 1851 had a marker pattern consistent with allotetraploidy and uniparental loss of one 18S-26S rDNA locus. This allotetraploid has previously been suggested to have originated from a hybrid with Festucaglaucescens (Festucaarundinaceavar.glaucescens Boissier, 1844). However, the distribution patterns of the two rDNA sequences in this allotetraploid do not align with F.glaucescens, suggesting that its origin from this species is unlikely. Furthermore, comparisons with other higher alloploids in the complex indicate that F.simensis was a potential donor of two sub-genomes of allohexaploid Festucagigantea (Linnaeus) Villars, 1787. In the overall complex, the proximal locations of both rDNA markers were conserved among the diploid species. Two types of synteny of the two markers could, to a considerable extent, distinguish allo- and autogamous Lolium species. The ancestral parentage of the three Festuca allotetraploids has not yet been determined, but all three appear to have been sub-genome donors to the higher allopolypoids of sub-genus Schedonorus. Terminal locations of both the markers were absent from the diploids but were very frequently observed in the polyploids.
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Affiliation(s)
- Helal Ahmad Ansari
- AgResearch Ltd, Grasslands Research Centre, Palmerston North 4412, New ZealandGrasslands Research CentrePalmerston NorthNew Zealand
| | - Nicholas Ellison
- AgResearch Ltd, Grasslands Research Centre, Palmerston North 4412, New ZealandGrasslands Research CentrePalmerston NorthNew Zealand
| | - Alan Vincent Stewart
- PGG Wrightson Seeds, Kimihia Research Centre, 1375 Springs Road, RD4, Lincoln 7674, New ZealandKimihia Research CentreLincolnNew Zealand
| | - Warren Mervyn Williams
- AgResearch Ltd, Grasslands Research Centre, Palmerston North 4412, New ZealandGrasslands Research CentrePalmerston NorthNew Zealand
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Rodionov AV, Gnutikov AA, Nosov NN, Machs EM, Mikhaylova YV, Shneyer VS, Punina EO. Intragenomic Polymorphism of the ITS 1 Region of 35S rRNA Gene in the Group of Grasses with Two-Chromosome Species: Different Genome Composition in Closely Related Zingeria Species. PLANTS 2020; 9:plants9121647. [PMID: 33255786 PMCID: PMC7760792 DOI: 10.3390/plants9121647] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/20/2020] [Accepted: 11/22/2020] [Indexed: 11/16/2022]
Abstract
Zingeria (Poaceae) is a small genus that includes Z. biebersteiniana, a diploid species with the lowest chromosome number known in plants (2n = 4) as well as hexaploid Z. kochii and tetraploid Z. pisidica, and/or Z. trichopoda species. The relationship between these species and the other low-chromosomes species Colpodium versicolor are unclear. To explore the intragenomic polymorphism and genome composition of these species we examined the sequences of the internal transcribed spacer 1 of the 35S rRNA gene via NGS approach. Our study revealed six groups of ribotypes in Zingeria species. Their distribution confirmed the allopolyploid nature of Z. kochii, whose probable ancestors were Colpodium versicolor and Z. pisidica. Z. pisidica has 98% of rDNA characteristic only for this species, and about 0.3% of rDNA related to that of Z. biebersteiniana. We assume that hexaploid Z. kochii is either an old allopolyploid or a homodiploid that has lost most of the rRNA genes obtained from Z. biebersteiniana. In Z. trichopoda about 81% of rDNA is related to rDNA of Z. biebersteiniana and 19% of rDNA is derived from Poa diaphora sensu lato. The composition of the ribotypes of the two plants determined by a taxonomy specialist as Z. pisidica and Z. trichopoda is very different. Two singleton species are proposed on this base with ribotypes as discriminative characters. So, in all four studied Zingeria species, even if the morphological difference among the studied species was modest, the genomic constitution was significantly different, which suggests that these are allopolyploids that obtained genomes from different ancestors.
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Affiliation(s)
- Alexander V. Rodionov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (A.V.R.); (N.N.N.); (E.M.M.); (Y.V.M.); (E.O.P.)
- Biological Faculty, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Alexander A. Gnutikov
- Department of Genetic Resources of Oat, Barley, Rye, N.I. Vavilov Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia;
| | - Nikolai N. Nosov
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (A.V.R.); (N.N.N.); (E.M.M.); (Y.V.M.); (E.O.P.)
| | - Eduard M. Machs
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (A.V.R.); (N.N.N.); (E.M.M.); (Y.V.M.); (E.O.P.)
| | - Yulia V. Mikhaylova
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (A.V.R.); (N.N.N.); (E.M.M.); (Y.V.M.); (E.O.P.)
| | - Victoria S. Shneyer
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (A.V.R.); (N.N.N.); (E.M.M.); (Y.V.M.); (E.O.P.)
- Correspondence:
| | - Elizaveta O. Punina
- Laboratory of Biosystematics and Cytology, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia; (A.V.R.); (N.N.N.); (E.M.M.); (Y.V.M.); (E.O.P.)
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Borowska‐Zuchowska N, Kovarik A, Robaszkiewicz E, Tuna M, Tuna GS, Gordon S, Vogel JP, Hasterok R. The fate of 35S rRNA genes in the allotetraploid grass Brachypodium hybridum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1810-1825. [PMID: 32506573 PMCID: PMC7497271 DOI: 10.1111/tpj.14869] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 05/20/2020] [Accepted: 05/28/2020] [Indexed: 05/22/2023]
Abstract
Nucleolar dominance (ND) consists of the reversible silencing of 35S/45S rDNA loci inherited from one of the ancestors of an allopolyploid. The molecular mechanisms by which one ancestral rDNA set is selected for silencing remain unclear. We applied a combination of molecular (Southern blot hybridization and reverse-transcription cleaved amplified polymorphic sequence analysis), genomic (analysis of variants) and cytogenetic (fluorescence in situ hybridization) approaches to study the structure, expression and epigenetic landscape of 35S rDNA in an allotetraploid grass that exhibits ND, Brachypodium hybridum (genome composition DDSS), and its putative progenitors, Brachypodium distachyon (DD) and Brachypodium stacei (SS). In progenitor genomes, B. stacei showed a higher intragenomic heterogeneity of rDNA compared with B. distachyon. In all studied accessions of B. hybridum, there was a reduction in the copy number of S homoeologues, which was accompanied by their inactive transcriptional status. The involvement of DNA methylation in CG and CHG contexts in the silencing of the S-genome rDNA loci was revealed. In the B. hybridum allotetraploid, ND is stabilized towards the D-genome units, irrespective of the polyphyletic origin of the species, and does not seem to be influenced by homoeologous 35S rDNA ratios and developmental stage.
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Affiliation(s)
- Natalia Borowska‐Zuchowska
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental ProtectionFaculty of Natural SciencesUniversity of Silesia in KatowiceJagiellonska 28Katowice40‐032Poland
| | - Ales Kovarik
- Department of Molecular EpigeneticsInstitute of BiophysicsAcademy of Sciences of the Czech Republic, v.v.i.Královopolská 135Brno612 65Czech Republic
| | - Ewa Robaszkiewicz
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental ProtectionFaculty of Natural SciencesUniversity of Silesia in KatowiceJagiellonska 28Katowice40‐032Poland
| | - Metin Tuna
- Department of Field CropsFaculty of AgricultureTekirdag Namik Kemal UniversitySuleymanpasaTekirdag59030Turkey
| | | | - Sean Gordon
- US Department of Energy (DOE) Joint Genome Institute (JGI)BerkeleyCA94720USA
| | - John P. Vogel
- US Department of Energy (DOE) Joint Genome Institute (JGI)BerkeleyCA94720USA
- University CaliforniaBerkeley, BerkeleyCA94720USA
| | - Robert Hasterok
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental ProtectionFaculty of Natural SciencesUniversity of Silesia in KatowiceJagiellonska 28Katowice40‐032Poland
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Qin Q, Wang C, Zhou Y, Qin H, Zhao C, Yang L, Yu T, Liu S. Rapid Genomic and Epigenetic Alterations in Gynogenetic Carassius auratus Red Var. Derived from Distant Hybridization. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:433-442. [PMID: 32249338 DOI: 10.1007/s10126-020-09963-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 03/16/2020] [Indexed: 06/11/2023]
Abstract
Gynogenesis is an important reproductive mode in fish and is used fairly widely in genetic breeding. Gynogenetic offspring (2n = 100, abbreviated as GRCC) were generated through the distant hybridization of Carassius auratus red var. (2n = 100, RCC) (♀) × Megalobrama amblycephala (2n = 48, BSB) (♂), in which male and female individual both had normal gonadal development. To better understand genomic and epigenetic consequences of GRCC, fluorescence in situ hybridization, amplified fragment length polymorphism, and methylation-sensitive amplification polymorphism analysis were performed on GRCC and RCC. GRCC possess two sets of RCC-derived chromosomes and one to three microchromosomes, in which 30.44% of bands inherit these patterns from red crucian carp and blunt snout bream, and 24.12% of novel bands were found by amplified fragment length polymorphism analysis. In terms of methylation, the DNA methylation level of GRCC was lower than that of their parents, and 45.29% of methylation patterns in GRCC were altered compared with their parents. GRCC show a special genetic composition in the genome, in which genome-wide changes and the adjustment of DNA methylation levels and patterns occurred. The result revealed that genetic and epigenetic changes were rapidly triggered in gynogenetic fish that were derived from distant hybridization, showing a special genetic composition in the genome. This study provides new insights into fish genetic breeding and the evolutionary patterns of the vertebrate genome.
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Affiliation(s)
- Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chongqing Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Yuwei Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Huan Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Chun Zhao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Li Yang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Tingting Yu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, People's Republic of China.
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Mateikovich AP, Punina EO, Kopylov-Guskov YO, Nosov NN, Gudkova PD, Gnutikov AA, Machs EM, Mikhailova YV, Krapivskaya EE, Rodionov AV. ITS1–5.8S rDNA–ITS2 and trnL-trnF Sequences as Markers for the Study of Species Diversity of Altai Feather Grasses. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420040067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Paštová L, Belyayev A, Mahelka V. Molecular cytogenetic characterisation of Elytrigia ×mucronata, a natural hybrid of E. intermedia and E. repens (Triticeae, Poaceae). BMC PLANT BIOLOGY 2019; 19:230. [PMID: 31151385 PMCID: PMC6544950 DOI: 10.1186/s12870-019-1806-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 04/26/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Interspecific hybridisation resulting in polyploidy is one of the major driving forces in plant evolution. Here, we present data from the molecular cytogenetic analysis of three cytotypes of Elytrigia ×mucronata using sequential fluorescence (5S rDNA, 18S rDNA and pSc119.2 probes) and genomic in situ hybridisation (four genomic probes of diploid taxa, i.e., Aegilops, Dasypyrum, Hordeum and Pseudoroegneria). RESULTS The concurrent presence of Hordeum (descended from E. repens) and Dasypyrum + Aegilops (descended from E. intermedia) chromosome sets in all cytotypes of E. ×mucronata confirmed the assumed hybrid origin of the analysed plants. The following different genomic constitutions were observed for E. ×mucronata. Hexaploid plants exhibited three chromosome sets from Pseudoroegneria and one chromosome set each from Aegilops, Hordeum and Dasypyrum. Heptaploid plants harboured the six chromosome sets of the hexaploid plants and an additional Pseudoroegneria chromosome set. Nonaploid cytotypes differed in their genomic constitutions, reflecting different origins through the fusion of reduced and unreduced gametes. The hybridisation patterns of repetitive sequences (5S rDNA, 18S rDNA, and pSc119.2) in E. ×mucronata varied between and within cytotypes. Chromosome alterations that were not identified in the parental species were found in both heptaploid and some nonaploid plants. CONCLUSIONS The results confirmed that both homoploid hybridisation and heteroploid hybridisation that lead to the coexistence of four different haplomes within single hybrid genomes occur in Elytrigia allopolyploids. The chromosomal alterations observed in both heptaploid and some nonaploid plants indicated that genome restructuring occurs during and/or after the hybrids arose. Moreover, a specific chromosomal translocation detected in one of the nonaploids indicated that it was not a primary hybrid. Therefore, at least some of the hybrids are fertile. Hybridisation in Triticeae allopolyploids clearly and significantly contributes to genomic diversity. Different combinations of parental haplomes coupled with chromosomal alterations may result in the establishment of unique lineages, thus providing raw material for selection.
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Affiliation(s)
- Ladislava Paštová
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Charles University, Benátská 2, 128 01 Prague, Czech Republic
| | - Alexander Belyayev
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
| | - Václav Mahelka
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
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Rodionov AV, Amosova AV, Belyakov EA, Zhurbenko PM, Mikhailova YV, Punina EO, Shneyer VS, Loskutov IG, Muravenko OV. Genetic Consequences of Interspecific Hybridization, Its Role in Speciation and Phenotypic Diversity of Plants. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419030141] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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10
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Rodionov AV, Dobryakova KS, Punina EO. Polymorphic Sites in ITS1-5.8S rDNA-ITS2 Region in Hybridogenic Genus × Elyhordeum and Putative Interspecific Hybrids Elymus (Poaceae: Triticeae). RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418090120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Kalinka A, Achrem M. Reorganization of wheat and rye genomes in octoploid triticale (× Triticosecale). PLANTA 2018; 247:807-829. [PMID: 29234880 PMCID: PMC5856900 DOI: 10.1007/s00425-017-2827-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 12/03/2017] [Indexed: 06/01/2023]
Abstract
The analysis of early generations of triticale showed numerous rearrangements of the genome. Complexed transformation included loss of chromosomes, t-heterochromatin content changes and the emergence of retrotransposons in new locations. This study investigated certain aspects of genomic transformations in the early generations (F5 and F8) of the primary octoploid triticale derived from the cross of hexaploid wheat with the diploid rye. Most of the plants tested were hypoploid; among eliminated chromosomes were rye chromosomes 4R and 5R and variable number of wheat chromosomes. Wheat chromosomes were eliminated to a higher extent. The lower content of telomeric heterochromatin was also found in rye chromosomes in comparison with parental rye. Studying the location of selected retrotransposons from Ty1-copia and Ty3-gypsy families using fluorescence in situ hybridization revealed additional locations of these retrotransposons that were not present in chromosomes of parental species. ISSR, IRAP and REMAP analyses showed significant changes at the level of specific DNA nucleotide sequences. In most cases, the disappearance of certain types of bands was observed, less frequently new types of bands appeared, not present in parental species. This demonstrates the scale of genome rearrangement and, above all, the elimination of wheat and rye sequences, largely due to the reduction of chromosome number. With regard to the proportion of wheat to rye genome, the rye genome was more affected by the changes, thus this study was focused more on the rye genome. Observations suggest that genome reorganization is not finished in the F5 generation but is still ongoing in the F8 generation.
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Affiliation(s)
- Anna Kalinka
- Department of Cell Biology, Faculty of Biology, Institute for Research on Biodiversity, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland
- Faculty of Biology, Molecular Biology and Biotechnology Center, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland
| | - Magdalena Achrem
- Department of Cell Biology, Faculty of Biology, Institute for Research on Biodiversity, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland.
- Faculty of Biology, Molecular Biology and Biotechnology Center, University of Szczecin, Wąska 13, 71-415, Szczecin, Poland.
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Rodionov AV, Gnutikov AA, Kotsinyan AR, Kotseruba VV, Nosov NN, Punina EO, Rayko MP, Tyupa NB, Kim ES. ITS1–5.8S rDNA–ITS2 sequence in 35S rRNA genes as marker for reconstruction of phylogeny of grasses (Poaceae family). ACTA ACUST UNITED AC 2017. [DOI: 10.1134/s2079086417020062] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Punina EO, Machs EM, Krapivskaya EE, Rodionov AV. Polymorphic sites in transcribed spacers of 35S rRNA genes as an indicator of origin of the Paeonia cultivars. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417010112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Maciak S, Michalak K, Kale SD, Michalak P. Nucleolar Dominance and Repression of 45S Ribosomal RNA Genes in Hybrids between Xenopus borealis and X. muelleri (2n = 36). Cytogenet Genome Res 2016; 149:290-296. [PMID: 27728911 DOI: 10.1159/000450665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2016] [Indexed: 11/19/2022] Open
Abstract
Nucleolar dominance is a dramatic disruption in the formation of nucleoli and the expression of ribosomal RNA (rRNA) genes, characteristic of some plant and animal hybrids. Here, we report that F1 hybrids produced from reciprocal crosses between 2 sister species of Xenopus clawed frogs, X. muelleri and X. borealis, undergo nucleolar dominance somewhat distinct from a pattern previously reported in hybrids between phylogenetically more distant Xenopus species. Patterns of nucleolar development, 45S rRNA expression, and gene copy inheritance were investigated using a combination of immunostaining, pyrosequencing, droplet digital PCR, flow cytometry, and epigenetic inhibition. In X. muelleri × X. borealis hybrids, typically only 1 nucleolus is formed, and 45S rRNA genes are predominantly expressed from 1 progenitor's alleles, X. muelleri, regardless of the cross-direction. These changes are accompanied by an extensive (∼80%) loss of rRNA gene copies in the hybrids relative to their parents, with the transcriptionally underdominant variant (X. borealis) being preferentially lost. Chemical treatment of hybrid larvae with a histone deacetylase inhibitor resulted in a partial derepression of the underdominant variant. Together, these observations shed light on the genetic and epigenetic basis of nucleolar dominance as an underappreciated manifestation of genetic conflicts within a hybrid genome.
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Winterfeld G, Wölk A, Röser M. Genome evolution in alpine oat-like grasses through homoploid hybridization and polyploidy. AOB PLANTS 2016; 8:plw039. [PMID: 27255513 PMCID: PMC4940509 DOI: 10.1093/aobpla/plw039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 05/07/2016] [Indexed: 05/17/2023]
Abstract
Hybridization and polyploidization can radically impact genome organization from sequence level to chromosome structure. As a result, often in response to environmental change and species isolation, the development of novel traits can arise and will tend to result in the formation of homoploid or polyploid hybrid species. In this study we focus on evidence of hybridization and polyploidization by ascertaining the species parentage of the endemic alpine Helictotrichon parlatorei group. This group comprises five taxa; the diploids H. parlatorei, Helictotrichon setaceum subsp. setaceum and subsp. petzense, their putative hybrid Helictotrichon ×krischae and the hexaploid Helictotrichon sempervirens. For molecular analyses, cloned nuclear Topoisomerase VI genes of H. sempervirens and H. ×krischae were sequenced and compared with sequences of the diploids to estimate the evolutionary history in this group. In addition, detailed chromosome studies were carried out including fluorescence in situ hybridization (FISH) with 5S and 45S ribosomal and satellite DNA probes, and fluorochrome staining with chromomycin and DAPI. Two distinct types of Topoisomerase VI sequences were identified. One of them (SET) occurs in both subspecies of H. setaceum, the other (PAR) in H. parlatorei. Both types were found in H. ×krischae and H. sempervirens Karyotypes of H. parlatorei and H. setaceum could be distinguished by chromosomes with a clearly differentiated banding pattern of ribosomal DNAs. Both patterns occurred in the hybrid H. ×krischae Hexaploid H. sempervirens shares karyotype features with diploid H. parlatorei, but lacks the expected chromosome characteristics of H. setaceum, possibly an example of beginning diploidization after polyploidization. The geographic origin of the putative parental species and their hybrids and the possible biogeographical spread through the Alps are discussed.
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Affiliation(s)
- Grit Winterfeld
- Institute of Biology, Martin Luther University Halle-Wittenberg, Neuwerk 21, 06099 Halle, Germany
| | - Alexandra Wölk
- Institute of Biology, Martin Luther University Halle-Wittenberg, Neuwerk 21, 06099 Halle, Germany
| | - Martin Röser
- Institute of Biology, Martin Luther University Halle-Wittenberg, Neuwerk 21, 06099 Halle, Germany
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Michalak K, Maciak S, Kim YB, Santopietro G, Oh JH, Kang L, Garner HR, Michalak P. Nucleolar dominance and maternal control of 45S rDNA expression. Proc Biol Sci 2015; 282:20152201. [PMID: 26645200 PMCID: PMC4685780 DOI: 10.1098/rspb.2015.2201] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 11/10/2015] [Indexed: 12/17/2022] Open
Abstract
Using a system of interspecies hybrids, trihybrids, and recombinants with varying proportions of genomes from three distinct Xenopus species, we provide evidence for de novo epigenetic silencing of paternal 45 S ribosomal ribonucleic acid (rRNA) genes and their species-dependent expression dominance that escapes transcriptional inactivation after homologous recombination. The same pattern of imprinting is maintained in the offspring from mothers being genetic males (ZZ) sex-reversed to females, indicating that maternal control of ribosomal deoxyribonucleic acid (rDNA) expression is not sex-chromosome linked. Nucleolar dominance (nucleolus underdevelopment) in Xenopus hybrids appears to be associated with a major non-Mendelian reduction in the number of 45 S rDNA gene copies rather than a specific pattern of their expression. The loss of rRNA gene copies in F1 hybrids was non-random with respect to the parental species, with the transcriptionally dominant variant preferentially removed from hybrid zygotes. This dramatic disruption in the structure and function of 45 S rDNA impacts transcriptome patterns of small nucleolar RNAs and messenger RNAs, with genes from the ribosome and oxidative stress pathways being among the most affected. Unorthodoxies of rDNA inheritance and expression may be interpreted as hallmarks of genetic conflicts between parental genomes, as well as defensive epigenetic mechanisms employed to restore genome integrity.
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Affiliation(s)
- Katarzyna Michalak
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Sebastian Maciak
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA Institute of Biology, University of Bialystok, PL-15-245, Poland
| | - Young Bun Kim
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | | | - Jung Hun Oh
- Department of Medical Physics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Lin Kang
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Harold R Garner
- The Edward Via College of Osteopathic Medicine, Blacksburg, VA 24060, USA
| | - Pawel Michalak
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
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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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18
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Qin Q, Wang J, Wang Y, Liu Y, Liu S. Organization and variation analysis of 5S rDNA in gynogenetic offspring of Carassius auratus red var. (♀) × Megalobrama amblycephala (♂). BMC Genet 2015; 16:26. [PMID: 25879826 PMCID: PMC4373122 DOI: 10.1186/s12863-015-0186-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/02/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The offspring with 100 chromosomes (abbreviated as GRCC) have been obtained in the first generation of Carassius auratus red var. (abbreviated as RCC, 2n = 100) (♀) × Megalobrama amblycephala (abbreviated as BSB, 2n = 48) (♂), in which the females and unexpected males both are found. Chromosomal and karyotypic analysis has been reported in GRCC which gynogenesis origin has been suggested, but lack genetic evidence. RESULT Fluorescence in situ hybridization with species-specific centromere probes directly proves that GRCC possess two sets of RCC-derived chromosomes. Sequence analysis of the coding region (5S) and adjacent nontranscribed spacer (abbreviated as NTS) reveals that three types of 5S rDNA class (class I; class II and class III) in GRCC are completely inherited from their female parent (RCC), and show obvious base variations and insertions-deletions. Fluorescence in situ hybridization with the entire 5S rDNA probe reveals obvious chromosomal loci (class I and class II) variation in GRCC. CONCLUSIONS This paper provides directly genetic evidence that GRCC is gynogenesis origin. In addition, our result is also reveals that distant hybridization inducing gynogenesis can lead to sequence and partial chromosomal loci of 5S rDNA gene obvious variation.
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Affiliation(s)
- QinBo Qin
- Key Laboratory of Protein Chemistry and Developmental Biology of the State Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410018, People's Republic of China.
| | - Juan Wang
- Key Laboratory of Protein Chemistry and Developmental Biology of the State Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410018, People's Republic of China.
| | - YuDe Wang
- Key Laboratory of Protein Chemistry and Developmental Biology of the State Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410018, People's Republic of China.
| | - Yun Liu
- Key Laboratory of Protein Chemistry and Developmental Biology of the State Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410018, People's Republic of China.
| | - ShaoJun Liu
- Key Laboratory of Protein Chemistry and Developmental Biology of the State Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, 410018, People's Republic of China.
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Zozomová-Lihová J, Mandáková T, Kovaříková A, Mühlhausen A, Mummenhoff K, Lysak MA, Kovařík A. When fathers are instant losers: homogenization of rDNA loci in recently formed Cardamine × schulzii trigenomic allopolyploid. THE NEW PHYTOLOGIST 2014; 203:1096-1108. [PMID: 24916080 DOI: 10.1111/nph.12873] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 04/29/2014] [Indexed: 05/20/2023]
Abstract
Recently formed allopolyploids represent an excellent system to study the impacts of hybridization and genomic duplication on genome structure and evolution. Here we explored the 35SrRNA genes (rDNA) in the Cardamine × schulzii allohexaploid that was formed by two subsequent hybridization events within the past c. 150 yr. The rDNA loci were analyzed by cloning, next generation sequencing (NGS), RT-PCR and FISH methods. The primary C. × insueta triploid hybrid derived from C. rivularis (♀) and C. amara (♂) had gene ratios highly skewed towards maternal sequences. Similarly, C. × schulzii, originating from the secondary hybridization event involving C. × insueta (♀) and C. pratensis (♂), showed a reduction in paternal rDNA homeologs despite an excess of chromosomes inherited from C. pratensis. We also identified novel rDNA loci in C. × schulzii, suggesting that lost loci might be slowly reinstalled by translocation (but not recombination) of genes from partner genomes. Prevalent clonal propagation of allopolyploids, C. × insueta and C. × schulzii, indicates that concerted evolution of rDNA may occur in the absence of extensive meiotic cycles. Adoption of NGS in rDNA variant analysis is highly informative for deciphering the evolutionary histories of allopolyploid species with ongoing homogenization processes.
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Affiliation(s)
| | - Terezie Mandáková
- RG Plant Cytogenomics, CEITEC, Masaryk University, Brno, Czech Republic
| | - Alena Kovaříková
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | | | - Klaus Mummenhoff
- Department of Biology, University Osnabrueck, Osnabrueck, Germany
| | - Martin A Lysak
- RG Plant Cytogenomics, CEITEC, Masaryk University, Brno, Czech Republic
| | - Aleš Kovařík
- Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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Winterfeld G, Schneider J, Perner K, Röser M. Polyploidy and hybridization as main factors of speciation: complex reticulate evolution within the grass genus Helictochloa. Cytogenet Genome Res 2014; 142:204-25. [PMID: 24731950 DOI: 10.1159/000361002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2013] [Indexed: 11/19/2022] Open
Abstract
To study the origin and evolution of naturally occurring polyploids, we performed phylogenetic analyses of nuclear ribosomal DNA spacers combined with molecular cytogenetics in 55 accessions of 27 taxa of the oat genus Helictochloa. A complex pattern of reticulate evolution was revealed with many diploid species and extensive polyploidy up to 20x. Altogether 11 groups of internal transcribed spacer (ITS) sequences can be distinguished. Sequences from 1-3 different ITS lineages were detected in polyploids. Cytogenetic data allow reconstruction of 8 basic monoploid chromosome sets. Six of these genomes occur in different combinations in the polyploid species. Two genomes are only found in diploids. Our sequence and karyological data highlight the occurrence of autopolyploidy and allopolyploidy, provide new information about the evolutionary history of taxa, and allow a more accurate systematic treatment of the concerned species. The geographical distribution of the 11 ITS lineages distinguished is highly structured and points to an origin of the genus in western Asia, presumably in grasslands like steppes or mountain steppes and meadows. The evolutionary basal lineages are of Asian, Minor Asian and east Mediterranean distribution and are present also in North America. The western and central parts of the Mediterranean and northern Europe harbor the modern lineages.
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Affiliation(s)
- G Winterfeld
- Institute of Biology, Martin Luther University Halle-Wittenberg, Halle, Germany
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21
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Crhak Khaitova L, Werlemark G, Kovarikova A, Nybom H, Kovarik A. High penetrance of a pan-canina type rDNA family in intersection Rosa hybrids suggests strong selection of bivalent chromosomes in the section Caninae. Cytogenet Genome Res 2014; 143:104-13. [PMID: 24685720 DOI: 10.1159/000360437] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
All dogroses (Rosa sect. Caninae) are characterized by the peculiar canina meiosis in which genetic material is unevenly distributed between female and male gametes. The pan-canina rDNA family (termed beta) appears to be conserved in all dogroses analyzed so far. Here, we have studied rDNAs in experimental hybrids obtained from open pollination of F1 plants derived from 2 independent intersectional crosses between the pentaploid dogrose species (2n = 5x = 35) Rosa rubiginosa as female parent (producing 4x egg cells due to the unique asymmetrical canina meiosis) and the tetraploid (2n = 4x = 28) garden rose R. hybrida 'André Brichet' as male parent (producing 2x pollen after normal meiosis). We analyzed the structure of rDNA units by molecular methods [CAPS and extensive sequencing of internal transcribed spacers (ITS)] and determined the number of loci on chromosomes by FISH. FISH showed that R. rubiginosa and 'André Brichet' harbored 5 and 4 highly heteromorphic rDNA loci, respectively. In the second generation of hybrid lines, we observed a reduced number of loci (4 and 5 instead of the expected 6). In R. rubiginosa and 'André Brichet', 2-3 major ITS types were found which is consistent with a weak homogenization pressure maintaining high diversity of ITS types in this genus. In contrast to expectation (the null hypothesis of Mendelian inheritance of ITS families), we observed reduced ITS diversity in some individuals of the second generation which might derive from self-fertilization or from a backcross to R. rubiginosa. In these individuals, the pan-canina beta family appeared to be markedly enriched, while the paternal families were lost or diminished in copies. Although the mechanism of biased meiotic transmission of certain rDNA types is currently unknown, we speculate that the bivalent-forming chromosomes carrying the beta rDNA family exhibit extraordinary pairing efficiency and/or are subjected to strong selection in Caninae polyploids.
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Affiliation(s)
- Lucie Crhak Khaitova
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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22
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Wang J, Liu S, Xiao J, Tao M, Zhang C, Luo K, Liu Y. Evidence for the evolutionary origin of goldfish derived from the distant crossing of red crucian carp × common carp. BMC Genet 2014; 15:33. [PMID: 24628745 PMCID: PMC3995517 DOI: 10.1186/1471-2156-15-33] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 03/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Distant hybridization can generate transgressive hybrid phenotypes that lead to the formation of new populations or species with increased genetic variation. In this study, we produced an experimental hybrid goldfish (EG) by distant crossing of red crucian carp (Carassius auratus) × common carp (Cyprinus carpio) followed by gynogenesis. RESULTS We evaluated the phenotype, ploidy level, gonadal structure, and 5S rDNA of the EG. Diploid EG possessed a high level of genetic variation, which was stably inherited. In particular, the EG combined transgressive phenotypes, including a forked tail and shortened caudal peduncle, traits that are present in common goldfish. The EG and common goldfish share a number of morphological and genetic similarities. CONCLUSIONS Using the EG, we provide new evidence that goldfish originated from hybridization of red crucian carp × common carp.
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Affiliation(s)
| | - Shaojun Liu
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha 410081, China.
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Mandáková T, Marhold K, Lysak MA. The widespread crucifer species Cardamine flexuosa is an allotetraploid with a conserved subgenomic structure. THE NEW PHYTOLOGIST 2014; 201:982-992. [PMID: 24400905 DOI: 10.1111/nph.12567] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Accepted: 09/23/2013] [Indexed: 05/18/2023]
Abstract
The origin of Cardamine flexuosa (Wavy Bittercress) has been a conundrum for more than six decades. Here we identify its parental species, analyse its genome structure in comparison to parental genomes and describe intergenomic structural variations in C. flexuosa. Genomic in situ hybridization (GISH) and comparative chromosome painting (CCP) uncovered the parental genomes and the chromosome composition of C. flexuosa and its presumed diploid progenitors. Cardamine flexuosa is an allotetraploid (2n = 4x = 32), originating from two diploid species, Cardamine amara and Cardamine hirsuta (2n = 2x = 16). The two parental species display almost perfectly conserved chromosomal collinearity for seven out of the eight chromosomes. A 13 Mb pericentric inversion distinguishes chromosome CA1 from CH1. A comparative cytomolecular map was established for C. flexuosa by CCP/GISH. Whereas conserved chromosome collinearity between the C. amara and C. hirsuta subgenomes might have promoted intergenomic rearrangements through homeologous recombination, only one reciprocal translocation between two homeologues has occurred since the origin of C. flexuosa. The genome of C. flexuosa demonstrates that allopolyploids can maintain remarkably stable subgenomes over 10(4) -10(5) yr throughout a wide distribution range. By contrast, the rRNA genes underwent genome-specific elimination towards a diploid-like number of loci.
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Affiliation(s)
- Terezie Mandáková
- Plant Cytogenomics research group, Central European Institute of Technology (CEITEC), Masaryk University, CZ-62500, Brno, Czech Republic
| | - Karol Marhold
- Institute of Botany, Slovak Academy of Sciences, SK-84523, Bratislava, Slovakia
- Department of Botany, Faculty of Science, Charles University, CZ-12801, Prague, Czech Republic
| | - Martin A Lysak
- Plant Cytogenomics research group, Central European Institute of Technology (CEITEC), Masaryk University, CZ-62500, Brno, Czech Republic
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Punina EO, Machs EM, Krapivskaya EE, Kim ES, Mordak EV, Myakoshina YA, Rodionov AV. Interspecific hybridization in the genus Paeonia (Paeoniaceae): Polymorphic sites in transcribed spacers of the 45S rRNA genes as indicators of natural and artificial peony hybrids. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412070113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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He W, Qin Q, Liu S, Li T, Wang J, Xiao J, Xie L, Zhang C, Liu Y. Organization and variation analysis of 5S rDNA in different ploidy-level hybrids of red crucian carp × topmouth culter. PLoS One 2012; 7:e38976. [PMID: 22720007 PMCID: PMC3377697 DOI: 10.1371/journal.pone.0038976] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Accepted: 05/14/2012] [Indexed: 11/18/2022] Open
Abstract
Through distant crossing, diploid, triploid and tetraploid hybrids of red crucian carp (Carassius auratus red var., RCC♀, Cyprininae, 2n = 100) × topmouth culter (Erythroculter ilishaeformis Bleeker, TC♂, Cultrinae, 2n = 48) were successfully produced. Diploid hybrids possessed 74 chromosomes with one set from RCC and one set from TC; triploid hybrids harbored 124 chromosomes with two sets from RCC and one set from TC; tetraploid hybrids had 148 chromosomes with two sets from RCC and two sets from TC. The 5S rDNA of the three different ploidy-level hybrids and their parents were sequenced and analyzed. There were three monomeric 5S rDNA classes (designated class I: 203 bp; class II: 340 bp; and class III: 477 bp) in RCC and two monomeric 5S rDNA classes (designated class IV: 188 bp, and class V: 286 bp) in TC. In the hybrid offspring, diploid hybrids inherited three 5S rDNA classes from their female parent (RCC) and only class IV from their male parent (TC). Triploid hybrids inherited class II and class III from their female parent (RCC) and class IV from their male parent (TC). Tetraploid hybrids gained class II and class III from their female parent (RCC), and generated a new 5S rDNA sequence (designated class I-N). The specific paternal 5S rDNA sequence of class V was not found in the hybrid offspring. Sequence analysis of 5S rDNA revealed the influence of hybridization and polyploidization on the organization and variation of 5S rDNA in fish. This is the first report on the coexistence in vertebrates of viable diploid, triploid and tetraploid hybrids produced by crossing parents with different chromosome numbers, and these new hybrids are novel specimens for studying the genomic variation in the first generation of interspecific hybrids, which has significance for evolution and fish genetics.
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Affiliation(s)
- Weiguo He
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
| | - Qinbo Qin
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
| | - Shaojun Liu
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
- * E-mail:
| | - Tangluo Li
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
| | - Jing Wang
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
| | - Jun Xiao
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
| | - Lihua Xie
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
| | - Chun Zhang
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
| | - Yun Liu
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People’s Republic of China
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Polyphyly of the grass tribe Hainardieae (Poaceae: Pooideae): identification of its different lineages based on molecular phylogenetics, including morphological and cytogenetic characteristics. ORG DIVERS EVOL 2012. [DOI: 10.1007/s13127-012-0077-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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Louis VL, Despons L, Friedrich A, Martin T, Durrens P, Casarégola S, Neuvéglise C, Fairhead C, Marck C, Cruz JA, Straub ML, Kugler V, Sacerdot C, Uzunov Z, Thierry A, Weiss S, Bleykasten C, De Montigny J, Jacques N, Jung P, Lemaire M, Mallet S, Morel G, Richard GF, Sarkar A, Savel G, Schacherer J, Seret ML, Talla E, Samson G, Jubin C, Poulain J, Vacherie B, Barbe V, Pelletier E, Sherman DJ, Westhof E, Weissenbach J, Baret PV, Wincker P, Gaillardin C, Dujon B, Souciet JL. Pichia sorbitophila, an Interspecies Yeast Hybrid, Reveals Early Steps of Genome Resolution After Polyploidization. G3 (BETHESDA, MD.) 2012; 2:299-311. [PMID: 22384408 PMCID: PMC3284337 DOI: 10.1534/g3.111.000745] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 12/16/2011] [Indexed: 12/19/2022]
Abstract
Polyploidization is an important process in the evolution of eukaryotic genomes, but ensuing molecular mechanisms remain to be clarified. Autopolyploidization or whole-genome duplication events frequently are resolved in resulting lineages by the loss of single genes from most duplicated pairs, causing transient gene dosage imbalance and accelerating speciation through meiotic infertility. Allopolyploidization or formation of interspecies hybrids raises the problem of genetic incompatibility (Bateson-Dobzhansky-Muller effect) and may be resolved by the accumulation of mutational changes in resulting lineages. In this article, we show that an osmotolerant yeast species, Pichia sorbitophila, recently isolated in a concentrated sorbitol solution in industry, illustrates this last situation. Its genome is a mosaic of homologous and homeologous chromosomes, or parts thereof, that corresponds to a recently formed hybrid in the process of evolution. The respective parental contributions to this genome were characterized using existing variations in GC content. The genomic changes that occurred during the short period since hybrid formation were identified (e.g., loss of heterozygosity, unilateral loss of rDNA, reciprocal exchange) and distinguished from those undergone by the two parental genomes after separation from their common ancestor (i.e., NUMT (NUclear sequences of MiTochondrial origin) insertions, gene acquisitions, gene location movements, reciprocal translocation). We found that the physiological characteristics of this new yeast species are determined by specific but unequal contributions of its two parents, one of which could be identified as very closely related to an extant Pichia farinosa strain.
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Affiliation(s)
| | - Laurence Despons
- Université de Strasbourg, CNRS UMR7156, F-67000 Strasbourg, France
| | - Anne Friedrich
- Université de Strasbourg, CNRS UMR7156, F-67000 Strasbourg, France
| | - Tiphaine Martin
- Université de Bordeaux 1, LaBRI INRIA Bordeaux Sud-Ouest (MAGNOME), F-33405 Talence, France
| | - Pascal Durrens
- Université de Bordeaux 1, LaBRI INRIA Bordeaux Sud-Ouest (MAGNOME), F-33405 Talence, France
| | - Serge Casarégola
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Cécile Neuvéglise
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Cécile Fairhead
- Institut de Génétique et Microbiologie, Université Paris-Sud, UMR CNRS 8621, F-91405 Orsay CEDEX, France
| | - Christian Marck
- Institut de Biologie et de Technologies de Saclay (iBiTec-S), CEA, F-91191 Gif-sur-Yvette CEDEX, France
| | - José A. Cruz
- Université de Strasbourg, Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, F-67084 Strasbourg, France
| | | | - Valérie Kugler
- Université de Strasbourg, CNRS UMR7156, F-67000 Strasbourg, France
| | - Christine Sacerdot
- Institut Pasteur, CNRS URA2171, Université Pierre et Maris Curie, Paris 6 UFR927, F-75724, Paris-CEDEX 15, France
| | - Zlatyo Uzunov
- Sofia University St. Kliment Ohridski, Faculty of Biology, Department of General and Applied Microbiology, 1164, Sofia, Bulgaria
| | - Agnes Thierry
- Institut Pasteur, CNRS URA2171, Université Pierre et Maris Curie, Paris 6 UFR927, F-75724, Paris-CEDEX 15, France
| | - Stéphanie Weiss
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | | | | | - Noemie Jacques
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Paul Jung
- Université de Strasbourg, CNRS UMR7156, F-67000 Strasbourg, France
| | - Marc Lemaire
- Université de Lyon, F-69622, Lyon, France; Université Lyon 1, Villeurbanne; CNRS, UMR5240 Microbiologie, Adaptation et Pathogénie; INSA de Lyon, F-69621, Villeurbanne, France
| | - Sandrine Mallet
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Guillaume Morel
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Guy-Franck Richard
- Institut Pasteur, CNRS URA2171, Université Pierre et Maris Curie, Paris 6 UFR927, F-75724, Paris-CEDEX 15, France
| | - Anasua Sarkar
- Université de Bordeaux 1, CNRS UMR5800, F-33405 Talence, France
| | - Guilhem Savel
- Université de Bordeaux 1, CNRS UMR5800, F-33405 Talence, France
| | | | - Marie-Line Seret
- Earth and Life Institute, Université Catholique de Louvain, B-1348, Louvain-la-Neuve, Belgium
| | - Emmanuel Talla
- Université de la Méditerranée, Laboratoire de Chimie Bactérienne, CNRS-UPR9043, 31 chemin Joseph Aiguier, F-13402 Marseille CEDEX 20, France
| | - Gaelle Samson
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Claire Jubin
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Julie Poulain
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Benoît Vacherie
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Valérie Barbe
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Eric Pelletier
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - David J. Sherman
- Université de Bordeaux 1, LaBRI INRIA Bordeaux Sud-Ouest (MAGNOME), F-33405 Talence, France
| | - Eric Westhof
- Université de Strasbourg, Architecture et Réactivité de l’ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, F-67084 Strasbourg, France
| | - Jean Weissenbach
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Philippe V. Baret
- Earth and Life Institute, Université Catholique de Louvain, B-1348, Louvain-la-Neuve, Belgium
| | - Patrick Wincker
- CEA, DSV, IG, Génoscope; CNRS UMR 8030; Université d’Evry Val d’ Essonne, 2 rue Gaston Crémieux, F-91057 Evry, France
| | - Claude Gaillardin
- INRA UMR 1319 Micalis, AgroParisTech, Bat. CBAI, F-78850 Thiverval-Grignon, France
| | - Bernard Dujon
- Institut Pasteur, CNRS URA2171, Université Pierre et Maris Curie, Paris 6 UFR927, F-75724, Paris-CEDEX 15, France
| | - Jean-Luc Souciet
- Université de Strasbourg, CNRS UMR7156, F-67000 Strasbourg, France
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Matyasek R, Fulnecek J, Leitch AR, Kovarik A. Analysis of two abundant, highly related satellites in the allotetraploid Nicotiana arentsii using double-strand conformation polymorphism analysis and sequencing. THE NEW PHYTOLOGIST 2011; 192:747-59. [PMID: 21777247 DOI: 10.1111/j.1469-8137.2011.03827.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
• Allopolyploidy, a driving force in plant evolution, can induce rapid structural changes in parental subgenomes. Here, we examined the fate of homologous subtelomeric satellites in intrasection allotetraploid Nicotiana arentsii formed from N. undulata and N. wigandioides progenitors < 200,000 yr ago. • We cloned and sequenced a number of monomers from progenitors and the allotetraploid. Structural features of both cloned and genomic monomers were studied using double-strand conformation polymorphism analysis. • Two homologous satellites were isolated from N. undulata (called NUNSSP) and N. wigandioides (NWISSP). While the NUNSSP monomers were highly homogeneous in nucleotide sequences, the NWISSP monomers formed two separate clades. Likewise, the genomic NUNSSP monomers showed less DNA conformation heterogeneity than NWISSP monomers, with distinct conformations. While both satellites predominantly occupy subtelomeric positions, a fraction of the NWISSP repeats was found in an intercalary location, supporting the hypothesis that dispersion prevents the repeats becoming homogeneous. Sequence, structural and chromosomal features of the parental satellites were faithfully inherited by N. arentsii. • Our study revealed that intergenomic homogenization of subtelomeric satellite repeats does not occur in N. arentsii allotetraploid. We propose that the sequence and structural divergence of subtelomeric satellites may render allopolyploid chromosomes less vulnerable to intergenomic exchanges.
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Affiliation(s)
- Roman Matyasek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, vvi, Brno, Czech Republic.
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29
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Kolano B, Gardunia BW, Michalska M, Bonifacio A, Fairbanks D, Maughan PJ, Coleman CE, Stevens MR, Jellen EN, Maluszynska J. Chromosomal localization of two novel repetitive sequences isolated from the Chenopodium quinoa Willd. genome. Genome 2011; 54:710-7. [PMID: 21848446 DOI: 10.1139/g11-035] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The chromosomal organization of two novel repetitive DNA sequences isolated from the Chenopodium quinoa Willd. genome was analyzed across the genomes of selected Chenopodium species. Fluorescence in situ hybridization (FISH) analysis with the repetitive DNA clone 18-24J in the closely related allotetraploids C. quinoa and Chenopodium berlandieri Moq. (2n = 4x = 36) evidenced hybridization signals that were mainly present on 18 chromosomes; however, in the allohexaploid Chenopodium album L. (2n = 6x = 54), cross-hybridization was observed on all of the chromosomes. In situ hybridization with rRNA gene probes indicated that during the evolution of polyploidy, the chenopods lost some of their rDNA loci. Reprobing with rDNA indicated that in the subgenome labeled with 18-24J, one 35S rRNA locus and at least half of the 5S rDNA loci were present. A second analyzed sequence, 12-13P, localized exclusively in pericentromeric regions of each chromosome of C. quinoa and related species. The intensity of the FISH signals differed considerably among chromosomes. The pattern observed on C. quinoa chromosomes after FISH with 12-13P was very similar to GISH results, suggesting that the 12-13P sequence constitutes a major part of the repetitive DNA of C. quinoa.
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Affiliation(s)
- B Kolano
- Department of Plant Anatomy and Cytology, University of Silesia, Katowice, Poland.
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30
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Rodionov AV, Nosov NN, Kim ES, Machs EM, Punina EO, Probatova NS. The origin of polyploid genomes of bluegrasses Poa L. and Gene flow between northern pacific and sub-Antarctic Islands. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410120021] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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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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32
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Qin Q, He W, Liu S, Wang J, Xiao J, Liu Y. Analysis of 5S rDNA organization and variation in polyploid hybrids from crosses of different fish subfamilies. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2010; 314:403-11. [PMID: 20535772 DOI: 10.1002/jez.b.21346] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
In this article, sequence analysis of the coding region (5S) and adjacent nontranscribed spacer (NTS) were conducted in red crucian carp (RCC), blunt snout bream (BSB), and their polyploid offspring. Three monomeric 5S rDNA classes (designated class I: 203 bp; class II: 340 bp; and class III: 477 bp) of RCC were characterized by distinct NTS types (designated NTS-I, II, and III for the 83, 220, and 357 bp monomers, respectively). In BSB, only one monomeric 5S rDNA was observed (designated class IV: 188 bp), which was characterized by one NTS type (designated NTS-IV: 68 bp). In the polyploid offspring, the tetraploid (4nRB) hybrids partially inherited 5S rDNA classes from their female parent (RCC); however, they also possessed a unique 5S rDNA sequence (designated class I-L: 203 bp) with a novel NTS sequence (designated NTS-I-L: 83 bp). The characteristic paternal 5S rDNA sequences (class IV) were not observed. The 5S rDNA of triploid (3nRB) hybrids was completely inherited from the parental species, and generally preserved the parental 5S rDNA structural organization. These results first revealed the influence of polyploidy on the organization and evolution of the multigene family of 5S rDNA of fish, and are also useful in clarifying aspects of vertebrate genome evolution.
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Affiliation(s)
- Qinbo Qin
- Key Laboratory of Protein Chemistry and Fish Developmental Biology of Education Ministry of China, College of Life Sciences, Hunan Normal University, Changsha, People's Republic of China
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Anssour S, Baldwin IT. Variation in antiherbivore defense responses in synthetic Nicotiana allopolyploids correlates with changes in uniparental patterns of gene expression. PLANT PHYSIOLOGY 2010; 153:1907-18. [PMID: 20525855 PMCID: PMC2923876 DOI: 10.1104/pp.110.156786] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2010] [Accepted: 06/01/2010] [Indexed: 05/21/2023]
Abstract
We examined the expression of Nicotiana attenuata (Na) and Nicotiana obtusifolia (No) herbivore-induced genes in synthetic autopolyploids (NaT and NoT) and five independent allopolyploid Nicotiana x obtusiata (Nxo) lines to understand how the expression of genes regulating complex polygenetic defense traits is altered in the early stages of allopolyploid hybridization. In Na, applying Manduca sexta oral secretions (OS) to wounds rapidly increased the transcript accumulation of wound-induced protein kinase (WIPK), lipoxygenase 3 (LOX3), nonexpressor of pathogenesis-related 1 (NPR1), and jasmonate-resistant 4 (JAR4) genes; these were correlated with increases in accumulation of jasmonic acid (JA), jasmonate-isoleucine, and trypsin protease inhibitors (TPIs). In No, OS elicitation reduced NPR1 transcripts and increased the level of salicylic acid (SA) that appeared to antagonize JA and JA-mediated defenses. OS elicited Nxo lines, accumulated high levels of the uniparental transcript of WIPK, LOX3, JAR4, and TPI, but low levels of both parental NPR1 transcripts that in turn were correlated with an increase in SA and a decrease in JA levels, suggesting SA/JA antagonism in the allopolyploid crosses. Methyl jasmonate treatment of Nxo lines elicited transcripts of both parental LOX3, JAR4, and TPIs, demonstrating that the uniparental pattern observed after OS elicitation was not due to gene inactivation. TPIs were induced at different levels among Nxo lines; some lines expressed high levels comparable to Na, others low levels similar to No, suggesting that synthetic neoallopolyploids rapidly readjust the expression of their parental defensive genes to generate diverse antiherbivore responses. Changes in the expression of key genes and posttranscriptional events likely facilitate adaptive radiations during allopolyploid speciation events.
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Affiliation(s)
- Samir Anssour
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Beutenberg Campus, D-07745 Jena, Germany
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34
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Mahelka V, Kopecký D. Gene capture from across the grass family in the allohexaploid Elymus repens (L.) Gould (Poaceae, Triticeae) as evidenced by ITS, GBSSI, and molecular cytogenetics. Mol Biol Evol 2010; 27:1370-90. [PMID: 20106909 DOI: 10.1093/molbev/msq021] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Four accessions of hexaploid Elymus repens from its native Central European distribution area were analyzed using sequencing of multicopy (internal transcribed spacer, ITS) and single-copy (granule-bound starch synthase I, GBSSI) DNA in concert with genomic and fluorescent in situ hybridization (GISH and FISH) to disentangle its allopolyploid origin. Despite extensive ITS homogenization, nrDNA in E. repens allowed us to identify at least four distinct lineages. Apart from Pseudoroegneria and Hordeum, representing the major genome constituents, the presence of further unexpected alien genetic material, originating from species outside the Triticeae and close to Panicum (Paniceae) and Bromus (Bromeae), was revealed. GBSSI sequences provided information complementary to the ITS. Apart from Pseudoroegneria and Hordeum, two additional gene variants from within the Triticeae were discovered: One was Taeniatherum-like, but the other did not have a close relationship with any of the diploids sampled. GISH results were largely congruent with the sequence-based markers. GISH clearly confirmed Pseudoroegneria and Hordeum as major genome constituents and further showed the presence of a small chromosome segment corresponding to Panicum. It resided in the Hordeum subgenome and probably represents an old acquisition of a Hordeum progenitor. Spotty hybridization signals across all chromosomes after GISH with Taeniatherum and Bromus probes suggested that gene acquisition from these species is more likely due to common ancestry of the grasses or early introgression than to recent hybridization or allopolyploid origin of E. repens. Physical mapping of rDNA loci using FISH revealed that all rDNA loci except one minor were located on Pseudoroegneria-derived chromosomes, which suggests the loss of all Hordeum-derived loci but one. Because homogenization mechanisms seem to operate effectively among Pseudoroegneria-like copies in this species, incomplete ITS homogenization in our samples is probably due to an interstitial position of an individual minor rDNA locus located within the Hordeum-derived subgenome.
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Affiliation(s)
- Václav Mahelka
- Institute of Botany, Academy of Sciences of the Czech Republic, Průhonice, Czech Republic.
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35
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Kotseruba V, Pistrick K, Blattner FR, Kumke K, Weiss O, Rutten T, Fuchs J, Endo T, Nasuda S, Ghukasyan A, Houben A. The evolution of the hexaploid grass Zingeriakochii (Mez) Tzvel. (2n=12) was accompanied by complex hybridization and uniparental loss of ribosomal DNA. Mol Phylogenet Evol 2010; 56:146-55. [PMID: 20060916 DOI: 10.1016/j.ympev.2010.01.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Revised: 12/16/2009] [Accepted: 01/03/2010] [Indexed: 10/20/2022]
Abstract
In the grass tribe Poeae a small group of taxa occur with an exceptionally low chromosome number of 2n=2x=4 belonging to the closely related genera Colpodium and Zingeria. To understand the formation of polyploids in this group we analyzed the evolution of allohexaploid Zingeriakochii (2n=12) and its presumable ancestral species. Genomic insitu hybridization demonstrated that Z.kochii evolved from an interspecific hybrid involving species closely related to contemporary Z.biebersteiniana (2n=4) and Colpodiumversicolor (2n=4) and a third unknown species. Following allopolyploidization of Z.kochii the biebersteiniana-like parental chromosomes underwent loss of ribosomal DNA. No interlocus homogenization of 45S rDNA took place in Z.kochii and phylogenetic analysis showed that C.versicolor contributed its genome to Z.kochii relatively recently. Insitu hybridization was particularly effective in understanding the allopolyploid evolution in Zingeria while the analysis of ITS sequences alone would have resulted in a wrong interpretation of the allopolyploid history of the genus.
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36
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Garcia S, Garnatje T, Pellicer J, McArthur ED, Siljak-Yakovlev S, Vallès J. Ribosomal DNA, heterochromatin, and correlation with genome size in diploid and polyploid North American endemic sagebrushes (Artemisia, Asteraceae). Genome 2009; 52:1012-24. [DOI: 10.1139/g09-077] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Subgenus Tridentatae ( Artemisia , Asteraceae) can be considered a polyploid complex. Both polyploidy and hybridization have been documented in the Tridentatae. Fluorescent in situ hybridization (FISH) and fluorochrome banding were used to detect and analyze ribosomal DNA changes linked to polyploidization in this group by studying four diploid-polyploid species pairs. In addition, genome sizes and heterochromatin patterns were compared between these populations. The linked 5S and 35S rRNA genes are confirmed as characteristic for Artemisia, and a pattern at the diploid level of three rDNA loci located at telomeric positions proved to be typical. Loss of rDNA loci was observed in some polyploids, whereas others showed additivity with respect to their diploid relatives. Genome downsizing was observed in all polyploids. Banding patterns differed depending on the pair of species analysed, but some polyploid populations showed an increased number of heterochromatic bands. FISH and fluorochrome banding were useful in determining the systematic position of Artemisia bigelovii , for which a differential pattern was found as compared with the rest of the group. Additionally, FISH was used to detect the presence of the Arabidopsis-type telomere repeat for the first time in Artemisia.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
| | - Teresa Garnatje
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
| | - Jaume Pellicer
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
| | - E. Durant McArthur
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
| | - Sonja Siljak-Yakovlev
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
| | - Joan Vallès
- Institut Botànic de Barcelona (CSIC-ICUB), Passeig del Migdia s/n, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Catalonia, Spain
- Shrub Sciences Laboratory, Rocky Mountain Research Station, Forest Service, United States Department of Agriculture, Provo, UT 84606, USA
- Ecologie, Systématique et Evolution, UMR CNRS 8079, Université Paris-Sud, Bâtiment 360, 91405 Orsay CEDEX, France
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37
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Kim ES, Bolsheva NL, Samatadze TE, Nosov NN, Nosova IV, Zelenin AV, Punina EO, Muravenko OV, Rodionov AV. The unique genome of two-chromosome grasses Zingeria and Colpodium, its origin, and evolution. RUSS J GENET+ 2009. [DOI: 10.1134/s1022795409110076] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Bao Y, Wendel JF, Ge S. Multiple patterns of rDNA evolution following polyploidy in Oryza. Mol Phylogenet Evol 2009; 55:136-142. [PMID: 19857580 DOI: 10.1016/j.ympev.2009.10.023] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Revised: 10/06/2009] [Accepted: 10/18/2009] [Indexed: 10/20/2022]
Abstract
Ribosomal ITS sequences are commonly used for phylogenetic reconstruction because they are included in rDNA repeats, and hence are ubiquitous and present in high copy number. Ribosomal rDNA repeats often undergo rapid concerted evolution within and between arrays. Interspecific hybridization merges divergent repeat types in a single nucleus, setting in motion evolutionary processes leading to coexistence, maintenance of paralogs, origin of novel sequence variants, loss of arrays, or inter-array sequence homogenization via concerted evolution. Here we examined ITS polymorphism within and among six Oryza tetraploids of varying genomic composition to infer the extent and direction of concerted evolution following allopolyploid speciation. We demonstrate that different polyploids have experienced varying fates, including maintenance or homogenization of divergent arrays, even among allopolyploids having the same genomic origins but in different geographic locations. Bidirectional concerted evolution, in which arrays become homogenized to alternative progenitor diploid types in different allopolyploid derivatives, is evident among species in one clade. Our results exemplify the panoply of outcomes for ribosomal DNA evolution following allopolyploid speciation.
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Affiliation(s)
- Ying Bao
- College of Life Science, Qufu Normal University, Qufu, Shandong 273165, PR China; State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China.
| | - Jonathan F Wendel
- Department of Ecology, Evolution, & Organismal Biology, Iowa State University, Ames, IA 50011, United States
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
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Castiglione MR, Kotseruba V, Cremonini R. Methylated-rich regions and tandem repeat arrays along the chromosome complement of Colpodium versicolor (Stev.) Schmalh. PROTOPLASMA 2009; 237:13-18. [PMID: 19621206 DOI: 10.1007/s00709-009-0063-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2009] [Accepted: 07/02/2009] [Indexed: 05/26/2023]
Abstract
The grass Colpodium versicolor (Stev.) Schmalh is one of six angiosperms with extremely reduced chromosome set 2n = 2x = 4. The chromosome complement of this species was studied. The DNA methylation pattern was determined with a specific monoclonal antiboby. 5-Methylcytosine residues are present in different chromosomal sites, with specific occurrence, some methylated bands showing differences between homologous chromosomes. Moreover, a fluorescent in situ hybridisation with telomere repeats and 45S rDNA sequences were performed. Hybridisation signals of telomeric repeats are detectable at the distal ends of the two pair of chromosomes, while 45S rDNA is localised in one chromosomal site, corresponding to the secondary constriction. In addition, 45S rDNA, as well as telomere-associated sequences, results to be 5-methylcytosine-enriched. The results are discussed and compared with those previously obtained in other plant systems 2n = 4 with the aim to enable a better knowledge of the lengthwise differentiation of this chromosome complement.
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Allopolyploid origin of Mediterranean species inHelictotrichon(Poaceae) and its consequences for karyotype repatterning and homogenisation of rDNA repeat units. SYST BIODIVERS 2009. [DOI: 10.1017/s1477200009003041] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Anssour S, Krügel T, Sharbel TF, Saluz HP, Bonaventure G, Baldwin IT. Phenotypic, genetic and genomic consequences of natural and synthetic polyploidization of Nicotiana attenuata and Nicotiana obtusifolia. ANNALS OF BOTANY 2009; 103:1207-17. [PMID: 19307190 PMCID: PMC2685307 DOI: 10.1093/aob/mcp058] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2008] [Revised: 01/19/2009] [Accepted: 02/02/2009] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND METHODS Polyploidy results in genetic turmoil, much of which is associated with new phenotypes that result in speciation. Five independent lines of synthetic allotetraploid N. x obtusiata (N x o) were created from crosses between the diploid N. attenuata (Na) (male) and N. obtusifolia (No) (female) and the autotetraploids of Na (NaT) and No (NoT) were synthesized. Their genetic, genomic and phenotypic changes were then compared with those of the parental diploid species (Na and No) as well as to the natural allotetraploids, N. quadrivalvis (Nq) and N. clevelandii (Nc), which formed 1 million years ago from crosses between ancient Na and No. KEY RESULTS DNA fingerprinting profiles (by UP-PCR) revealed that the five N x o lines shared similar but not identical profiles. Both synthetic and natural polyploidy showed a dosage effect on genome size (as measured in seeds); however, only Nq was associated with a genome upsizing. Phenotypic analysis revealed that at the cellular level, N x o lines had phenotypes intermediate of the parental phenotypes. Both allo- and autotetraploidization had a dosage effect on seed and dry biomass (except for NaT), but not on stalk height at first flower. Nc showed paternal (Na) cellular phenotypes but inherited maternal (No) biomass and seed mass, whereas Nq showed maternal (No) cellular phenotypes but inherited paternal (Na) biomass and seed mass patterns. Principal component analysis grouped Nq with N x o lines, due to similar seed mass, stalk height and genome size. These traits separated Nc, No and Na from Nq and N x o lines, whereas biomass distinguished Na from N x o and Nq lines, and NaT clustered closer to Nq and N x o lines than to Na. CONCLUSIONS Both allo- and autotetraploidy induce considerable morphological, genetic and genomic changes, many of which are retained by at least one of the natural polyploids. It is proposed that both natural and synthetic polyploids are well suited for studying the evolution of adaptive responses.
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Affiliation(s)
- S. Anssour
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Beutenberg Campus, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - T. Krügel
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Beutenberg Campus, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - T. F. Sharbel
- Apomixis Research Group, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
| | - H. P. Saluz
- Leibniz Institute for Natural Product Research and Infection Biology e.V, Hans-Knöll-Institute (HKI) Beutenbergstr. 11a, 07745 Jena, Germany
| | - G. Bonaventure
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Beutenberg Campus, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - I. T. Baldwin
- Max Planck Institute for Chemical Ecology, Department of Molecular Ecology, Beutenberg Campus, Hans-Knöll-Str. 8, 07745 Jena, Germany
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Nakao Y, Kanamori T, Itoh T, Kodama Y, Rainieri S, Nakamura N, Shimonaga T, Hattori M, Ashikari T. Genome sequence of the lager brewing yeast, an interspecies hybrid. DNA Res 2009; 16:115-29. [PMID: 19261625 PMCID: PMC2673734 DOI: 10.1093/dnares/dsp003] [Citation(s) in RCA: 231] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This work presents the genome sequencing of the lager brewing yeast (Saccharomyces pastorianus) Weihenstephan 34/70, a strain widely used in lager beer brewing. The 25 Mb genome comprises two nuclear sub-genomes originating from Saccharomyces cerevisiae and Saccharomyces bayanus and one circular mitochondrial genome originating from S. bayanus. Thirty-six different types of chromosomes were found including eight chromosomes with translocations between the two sub-genomes, whose breakpoints are within the orthologous open reading frames. Several gene loci responsible for typical lager brewing yeast characteristics such as maltotriose uptake and sulfite production have been increased in number by chromosomal rearrangements. Despite an overall high degree of conservation of the synteny with S. cerevisiae and S. bayanus, the syntenies were not well conserved in the sub-telomeric regions that contain lager brewing yeast characteristic and specific genes. Deletion of larger chromosomal regions, a massive unilateral decrease of the ribosomal DNA cluster and bilateral truncations of over 60 genes reflect a post-hybridization evolution process. Truncations and deletions of less efficient maltose and maltotriose uptake genes may indicate the result of adaptation to brewing. The genome sequence of this interspecies hybrid yeast provides a new tool for better understanding of lager brewing yeast behavior in industrial beer production.
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Affiliation(s)
- Yoshihiro Nakao
- R&D Planning Division, Suntory Limited, 1-1-1 Wakayamadai, Shimamoto-cho, Mishima-gun, Osaka, Japan.
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Maksimović M, Vidic D, Miloš M, Edita Šolić M, Abadžić S, Siljak-Yakovlev S. Effect of the environmental conditions on essential oil profile in two Dinaric Salvia species: S. brachyodon Vandas and S. officinalis L. BIOCHEM SYST ECOL 2007. [DOI: 10.1016/j.bse.2007.02.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Lim KY, Matyasek R, Kovarik A, Leitch A. Parental origin and genome evolution in the allopolyploid Iris versicolor. ANNALS OF BOTANY 2007; 100:219-24. [PMID: 17591610 PMCID: PMC2735315 DOI: 10.1093/aob/mcm116] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Revised: 03/26/2007] [Accepted: 05/01/2007] [Indexed: 05/16/2023]
Abstract
BACKGROUND AIMS One of the classic examples of an allopolyploid is Iris versicolor, 'Blue Flag' (2n = 108), first studied by Edgar Anderson and later popularized by George Ledyard Stebbins in cytogenetics and evolutionary text-books. It is revisited here using modern molecular and cytogenetic tools to investigate its putative allopolyploid origin involving progenitors of I. virginica (2n = 70) and I. setosa (2n = 38). METHODS Genomic in situ hybridization (GISH), fluorescent in situ hybridization (FISH) and Southern hybridization with 5S and 18-26S ribosomal DNA (rDNA) probes were used to identify the parental origin of chromosomes, and to study the unit structure, relative abundance and chromosomal location of rDNA sequences. KEY RESULTS GISH shows that I. versicolor has inherited the sum of the chromosome complement from the two progenitor species. In I. versicolor all the 18-26S rDNA units and loci are inherited from the progenitor of I. virginica, those loci from the I. setosa progenitor are absent. In contrast 5S rDNA loci and units from both progenitors are found, although one of the two 5S loci expected from the I. setosa progenitor is absent. CONCLUSIONS These data confirm Anderson's hypothesis that I. versicolor is an allopolyploid involving progenitors of I. virginica and I. setosa. The number of 18-26S rDNA loci in I. versicolor is similar to that of progenitor I. virginica, suggestive of a first stage in genome diploidization. The locus loss is targeted at the I. setosa-origin subgenome, and this is discussed in relation to other polyploidy systems.
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Affiliation(s)
- K Yoong Lim
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK.
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Pecinka A, Suchánková P, Lysak MA, Trávnícek B, Dolezel J. Nuclear DNA content variation among Central European Koeleria taxa. ANNALS OF BOTANY 2006; 98:117-22. [PMID: 16698888 PMCID: PMC2803546 DOI: 10.1093/aob/mcl077] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Revised: 01/17/2006] [Accepted: 03/03/2006] [Indexed: 05/09/2023]
Abstract
BACKGROUND AND AIMS Polyploidization plays an important role in the evolution of many plant genera, including Koeleria. The knowledge of ploidy, chromosome number and genome size may enable correct taxonomic treatment when other features are insufficient as in Koeleria. Therefore, these characteristics and their variability were determined for populations of six central European Koeleria taxa. METHODS Chromosome number analysis was performed by squashing root meristems, and ploidy and 2C nuclear DNA content were estimated by flow cytometry. KEY RESULTS Three diploids (K. glauca, K. macrantha var. macrantha and var. pseudoglauca), one tetraploid (K. macrantha var. majoriflora), one decaploid (K. pyramidata) and one dodecaploid (K. tristis) were found. The 2C nuclear DNA content of the diploids ranged from 4.85 to 5.20 pg. The 2C DNA contents of tetraploid, decaploid and dodecaploid taxa were 9.31 pg, 22.89 pg and 29.23 pg, respectively. The DNA content of polyploids within the K. macrantha aggregate (i.e. within K. macrantha and K. pyramidata) was smaller than the expected multiple of the diploid genome (K. macrantha var. macrantha). Geography-correlated variation of DNA content was found for some taxa. Czech populations of K. macrantha var. majoriflora had a 5.06% smaller genome than the Slovak ones. An isolated eastern Slovakian population of K. tristis revealed 8.04% less DNA than populations from central Slovakia. In central and north-west Bohemia, diploid and tetraploid cytotypes of K. macrantha were sympatric; east from this region diploid populations, and towards the west tetraploid populations were dominant. CONCLUSIONS Remarkable intra-specific inter-population differences in nuclear DNA content were found between Bohemian and Pannonian populations of Koeleria macrantha var. majoriflora and between geographically isolated central and eastern Slovakian populations of K. tristis. These differences occur over a relatively small geographical scale.
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Affiliation(s)
- Ales Pecinka
- Institute for Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, Gatersleben, D-06466, Germany.
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Ma XF, Gustafson JP. Genome evolution of allopolyploids: a process of cytological and genetic diploidization. Cytogenet Genome Res 2005; 109:236-49. [PMID: 15753583 DOI: 10.1159/000082406] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2003] [Accepted: 03/09/2004] [Indexed: 11/19/2022] Open
Abstract
Allopolyploidy is a prominent mode of speciation in higher plants. Due to the coexistence of closely related genomes, a successful allopolyploid must have the ability to invoke and maintain diploid-like behavior, both cytologically and genetically. Recent studies on natural and synthetic allopolyploids have raised many discrepancies. Most species have displayed non-Mendelian behavior in the allopolyploids, but others have not. Some species have demonstrated rapid genome changes following allopolyploid formation, while others have conserved progenitor genomes. Some have displayed directed, non-random genome changes, whereas others have shown random changes. Some of the genomic changes have appeared in the F1 hybrids, which have been attributed to the union of gametes from different progenitors, while other changes have occurred during or after genome doubling. Although these observations provide significant novel insights into the evolution of allopolyploids, the overall mechanisms of the event are still elusive. It appears that both genetic and epigenetic operations are involved in the diploidization process of allopolyploids. Overall, genetic and epigenetic variations are often associated with the activities of repetitive sequences and transposon elements. Specifically, genomic sequence elimination and chromosome rearrangement are probably the major forces guiding cytological diploidization. Gene non-functionalization, sub-functionalization, neo-functionalization, as well as other kinds of epigenetic modifications, are likely the leading factors promoting genetic diploidization.
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Affiliation(s)
- X-F Ma
- Department of Agronomy, University of Missouri-Columbia, MO 65211, USA
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Abstract
A survey is given about the number and chromosomal position of rDNA loci in 45 Brassicaceae species. For 34 species, 5S and 45S rDNA loci have been localized by two-colour fluorescence in situ hybridization for the first time. These data show the variability of rDNA within karyotypes of the Brassicaceae, provide anchor points for (comparative) genetic maps, and might be important for studies on concerted evolution of internal transcribed sequence types of rDNA in cruciferous plants.
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Affiliation(s)
- Hoda B M Ali
- Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Siljak-Yakovlev S, Solic ME, Catrice O, Brown SC, Papes D. Nuclear DNA content and chromosome number in some diploid and tetraploid Centaurea (Asteraceae: Cardueae) from the Dalmatia region. PLANT BIOLOGY (STUTTGART, GERMANY) 2005; 7:397-404. [PMID: 16025412 DOI: 10.1055/s-2005-865693] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Given the paucity of information about genome size in the genus Centaurea, nuclear DNA content of 15 Centaurea taxa, belonging to four subgenera and six different sections, has been investigated for the first time. The sample concerns 21 populations from the Dalmatia region of Croatia. The 2C DNA content and GC percentage were assessed by flow cytometry and chromosome number was determined using standard methods. Genome size of studied Centaurea ranged from 2C=1.67 to 3.72 pg. These results were in accordance with chromosome number and especially with ploidy level that varies throughout this group; 2C DNA values ranged from 1.67 to 3.43 pg for diploid, and from 3.19 to 3.72 for polyploid taxa. No significant intraspecific variations of DNA amount were found between two subspecies of C. visiani and C. ragusina, nor between two varieties of C. gloriosa. However, some populations of C. glaberrima and C. cuspidata showed a significant difference in DNA amount. Three different basic chromosome numbers were observed in studied species (x=9, 10, and 11). The most frequent basic number was x=9. C. rupestris, C. ragusina ssp. ragusina, and C. r. ssp. lungensis possessed x=10 and C. tuberosa x=11. The species with a basic chromosome number of x=9 had a small genome size and the smallest chromosomes (on average 0.09 to 0.12 pg/chromosome) but frequently present polyploidy. Centaurea ragusina ssp. ragusina and C. r. ssp. lungensis had a mean base composition 41.3% GC.
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Affiliation(s)
- S Siljak-Yakovlev
- Département Evolution et Systématique, UMR CNRS 8079, Université Paris-Sud, Bât. 360, 91405 Orsay Cedex, France.
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Genomic Configuration of the Autotetraploid Oat Species Avena macrostachya Inferred from Comparative Analysis of ITS1 and ITS2 Sequences: on the Oat Karyotype Evolution during the Early Events of the Avena Species Divergence. RUSS J GENET+ 2005. [DOI: 10.1007/s11177-005-0120-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Skalická K, Lim KY, Matyasek R, Matzke M, Leitch AR, Kovarik A. Preferential elimination of repeated DNA sequences from the paternal, Nicotiana tomentosiformis genome donor of a synthetic, allotetraploid tobacco. THE NEW PHYTOLOGIST 2005; 166:291-303. [PMID: 15760371 DOI: 10.1111/j.1469-8137.2004.01297.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Nicotiana tabacum (tobacco, 2n = 4x = 48) is a natural allotetraploid combining two ancestral genomes closely related to modern Nicotiana sylvestris and Nicotiana tomentosiformis. Here we examine the immediate consequences of allopolyploidy on genome evolution using 20 S4-generation plants derived from a single synthetic, S0 plant made by Burk in 1973 (Th37). Using molecular and cytogenetic methods we analysed 14 middle and highly repetitive sequences that together total approximately 4% of the genome. Two repeats related to endogenous geminiviruses (GRD5) and pararetroviruses (NtoEPRV), and two classes of satellite repeats (NTRS, A1/A2) were partially or completely eliminated at variable frequency (25-60%). These sequences are all from the N. tomentosiformis parent. Genomic in situ hybridization revealed additivity in chromosome numbers in two plants (2n = 48), while a third was aneuploid for an N. tomentosiformis-origin chromosome (2n = 49). Two plants had homozygous translocations between chromosomes of the S- and T-genomes. * The data demonstrate that genetic changes in synthetic tobacco were fast, targeted to the paternal N. tomentosiformis-donated genome, and some of the changes showed concordance with changes that presumably occurred during evolution of natural tobacco.
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Affiliation(s)
- K Skalická
- Institute of Biophysics, Academy of Sciences of the Czech Republic, CZ-61265 Brno, Czech Republic
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