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Krawczyk K, Nobis M, Nowak A, Szczecińska M, Sawicki J. Phylogenetic implications of nuclear rRNA IGS variation in Stipa L. (Poaceae). Sci Rep 2017; 7:11506. [PMID: 28912548 PMCID: PMC5599551 DOI: 10.1038/s41598-017-11804-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 08/25/2017] [Indexed: 01/03/2023] Open
Abstract
The article takes up the problem of deficiency of molecular marker, which could illustrate molecular variability as well as phylogenetic relation within the genus of Stipa L. (Poaceae). Researches made so far hadn’t delivered sufficient information about relationships between particular taxa from the genus of Stipa. In the present study, we analyzed variability and phylogenetic informativeness of nuclear ribosomal DNA in six species from the genus against five other species from Poaceae including a division of this region into functional elements and domains. Our results showed that the intergenic spacer region, and especially its part adjacent to 26 S nrDNA, is a molecular marker giving a real chance for a phylogeny reconstruction of Stipa. The region seems to be the most phylogenetically informative for Stipa from all the chloroplast and nuclear markers tested so far. Comparative analysis of nrDNA repeat units from Stipa to other representatives of Poaceae showed that their structure does not deviate from the general scheme. However, the rate of evolution within the inter-repeats in the IGS region is extremely high and therefore it predestines the region for phylogenetic analyses of Stipa at genus level or in shallower taxonomic scale.
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Affiliation(s)
- Katarzyna Krawczyk
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology and Earth Sciences, Jagiellonian University, Kraków, Poland
| | - Arkadiusz Nowak
- Polish Academy of Sciences Botanical Garden - Center for Biological Diversity Conservation in Powsin, Warsaw, Poland
| | - Monika Szczecińska
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Jakub Sawicki
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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Hinsinger DD, Gaudeul M, Couloux A, Bousquet J, Frascaria-Lacoste N. The phylogeography of Eurasian Fraxinus species reveals ancient transcontinental reticulation. Mol Phylogenet Evol 2014; 77:223-37. [PMID: 24795215 DOI: 10.1016/j.ympev.2014.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 04/14/2014] [Accepted: 04/18/2014] [Indexed: 01/16/2023]
Abstract
To investigate the biogeographical history of ashes species of the Eurasian section Fraxinus and to test the hypothesis of ancient reticulations, we sequenced nuclear DNA (nETS and nITS, 1075 bp) for 533 samples and scored AFLP for 63 samples of Eurasian ashes within the section Fraxinus. The nITS phylogeny retrieved the classical view of the evolution of the section, whereas nETS phylogeny indicated an unexpected separation of F. angustifolia in two paraphyletic groups, respectively found in southeastern Europe and in the other parts of the Mediterranean basin. In the nETS phylogeny, the former group was closely related to F. excelsior, whereas the later was closely related to F. mandshurica, a species which is restricted nowadays to northeastern Asia. This topological incongruence between the two loci indicated the occurrence of an ancient reticulation between European and Asian ash species. Several other ancient reticulation events between the two European species and the other species of the section were supported by the posterior predictive checking method. Some of these reticulation events would have occurred during the Miocene, when climatic variations may have lead these species to expand their distribution range and come into contact. The recurrent reticulations observed among Eurasian ash species indicate that they should be considered as conspecific taxa, with subspecific status for some groups. Altogether, the results of the present study provide a rare documented evidence for the occurrence of multiple ancient reticulations within a group of temperate tree taxa with modern disjunct distributions in Eurasia. These ancient reticulation events indicate that the speciation process is slow in ashes, necessitating long periods of geographical isolation. The implications for speciation processes in temperate trees with similar life history and reproductive biology are discussed.
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Affiliation(s)
- Damien D Hinsinger
- AgroParisTech, UMR 8079, 91405 Orsay, France; Centre national de la recherche scientifique, UMR 8079, 910405 Orsay, France; Université Paris-Sud, UMR 8079, F-91000 Orsay, France; Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt et Institut de biologie intégrative et des systèmes, Université Laval, Québec, Québec G1V 0A6, Canada.
| | - Myriam Gaudeul
- Muséum National d'Histoire Naturelle, UMR CNRS 7205 'Origine, Structure et Evolution de la Biodiversité', 16 rue Buffon, CP 39, F-75005 Paris, France.
| | - Arnaud Couloux
- Genoscope, Centre National de Séquençage, 2 rue Gaston Crémieux, CP 5706, F-91057 Evry Cedex, France.
| | - Jean Bousquet
- Chaire de recherche du Canada en génomique forestière et environnementale, Centre d'étude de la forêt et Institut de biologie intégrative et des systèmes, Université Laval, Québec, Québec G1V 0A6, Canada.
| | - Nathalie Frascaria-Lacoste
- AgroParisTech, UMR 8079, 91405 Orsay, France; Centre national de la recherche scientifique, UMR 8079, 910405 Orsay, France; Université Paris-Sud, UMR 8079, F-91000 Orsay, France.
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Ruffini Castiglione M, Gelati MT, Cremonini R, Frediani M. The intergenic spacer region of the rDNA in Haplopappus gracilis (Nutt.) Gray. PROTOPLASMA 2013; 250:683-689. [PMID: 22948831 DOI: 10.1007/s00709-012-0441-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 07/24/2012] [Indexed: 06/01/2023]
Abstract
In this paper, we provide further information on the genome organisation of Haplopappus gracilis, one of the six angiosperms showing the lowest chromosome number, i.e. 2n = 4, by determining the nucleotide sequence of the intergenic spacer region of the ribosomal RNA genes and its cytological localization on metaphase chromosomes. DNA sequence analysis reveals the occurring of a product of 4,382 bp in length, characterised by the presence of four blocks of different repeated sequences. Our analysis also evidenced putative promoter regions with three transcription initiation sites for polymerase I, as previously reported in Artemisia absinthium, belonging to the same Asteraceae family. A fluorescent in situ hybridization with the intergenic spacer probe indicates the presence of rDNA genes only in the satellited chromosomes of H. gracilis; besides, differences in the signal intensity between homologous chromosomes were frequently observed, thus suggesting for these chromosome sites the presence of a variable number of rDNA gene copies, even if a divergent chromatin organisation in corresponding regions cannot be ruled out.
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MESH Headings
- Base Sequence
- Chromosome Mapping
- Chromosomes, Plant
- DNA, Ribosomal Spacer/genetics
- Genes, Plant
- Haplopappus/genetics
- Molecular Sequence Annotation
- Molecular Sequence Data
- Promoter Regions, Genetic
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 5.8S/genetics
- Sequence Analysis, DNA
- Transcription Initiation Site
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Ambrose CD, Crease TJ. Evolution of the nuclear ribosomal DNA intergenic spacer in four species of the Daphnia pulex complex. BMC Genet 2011; 12:13. [PMID: 21261945 PMCID: PMC3036644 DOI: 10.1186/1471-2156-12-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Accepted: 01/24/2011] [Indexed: 12/24/2022] Open
Abstract
Background Concerted evolution refers to the pattern in which copies of multigene families show high intraspecific sequence homogeneity but high interspecific sequence diversity. Sequence homogeneity of these copies depends on relative rates of mutation and recombination, including gene conversion and unequal crossing over, between misaligned copies. The internally repetitive intergenic spacer (IGS) is located between the genes for the 28S and 18S ribosomal RNAs. To identify patterns of recombination and/or homogenization within IGS repeat arrays, and to identify regions of the IGS that are under functional constraint, we analyzed 13 complete IGS sequences from 10 individuals representing four species in the Daphnia pulex complex. Results Gene conversion and unequal crossing over between misaligned IGS repeats generates variation in copy number between arrays, as has been observed in previous studies. Moreover, terminal repeats are rarely involved in these events. Despite the occurrence of recombination, orthologous repeats in different species are more similar to one another than are paralogous repeats within species that diverged less than 4 million years ago. Patterns consistent with concerted evolution of these repeats were observed between species that diverged 8-10 million years ago. Sequence homogeneity varies along the IGS; the most homogeneous regions are downstream of the 28S rRNA gene and in the region containing the core promoter. The inadvertent inclusion of interspecific hybrids in our analysis uncovered evidence of both inter- and intrachromosomal recombination in the nonrepetitive regions of the IGS. Conclusions Our analysis of variation in ribosomal IGS from Daphnia shows that levels of homogeneity within and between species result from the interaction between rates of recombination and selective constraint. Consequently, different regions of the IGS are on substantially different evolutionary trajectories.
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Affiliation(s)
- Cheryl D Ambrose
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G2W1, Canada
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Ambrose CD, Crease TJ. Evolution of Repeated Sequences in the Ribosomal DNA Intergenic Spacer of 32 Arthropod Species. J Mol Evol 2010; 70:247-59. [DOI: 10.1007/s00239-010-9324-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 02/02/2010] [Indexed: 11/25/2022]
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Fehrer J, Krak K, Chrtek J. Intra-individual polymorphism in diploid and apomictic polyploid hawkweeds (Hieracium, Lactuceae, Asteraceae): disentangling phylogenetic signal, reticulation, and noise. BMC Evol Biol 2009; 9:239. [PMID: 19772642 PMCID: PMC2759941 DOI: 10.1186/1471-2148-9-239] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Accepted: 09/22/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hieracium s.str. is a complex species-rich group of perennial herbs composed of few sexual diploids and numerous apomictic polyploids. The existence of reticulation and the near-continuity of morphological characters across taxa seriously affect species determination, making Hieracium one of the best examples of a 'botanist's nightmare'. Consequently, its species relationships have not previously been addressed by molecular methods. Concentrating on the supposed major evolutionary units, we used nuclear ribosomal (ETS) and chloroplast (trnT-trnL) sequences in order to disentangle the phylogenetic relationships and to infer the origins of the polyploids. RESULTS Despite relatively low interspecific variation, the nuclear data revealed the existence of two major groups roughly corresponding to species with a Western or Eastern European origin. Extensive reticulation was mainly inferred from the character additivity of parental ETS variants. Surprisingly, many diploid species were of hybrid origin whilst several polyploid taxa showed no evidence of reticulation. Intra-individual ETS sequence polymorphism generally exceeded interspecific variation and was either independent of, or additional to, additive patterns accounted for by hybrid origin. Several ETS ribotypes occurred in different hybrid taxa, but never as the only variant in any species analyzed. CONCLUSION The high level of intra-individual ETS polymorphism prevented straightforward phylogenetic analysis. Characterization of this variation as additive, shared informative, homoplasious, or unique made it possible to uncover the phylogenetic signal and to reveal the hybrid origin of 29 out of 60 accessions. Contrary to expectation, diploid sexuals and polyploid apomicts did not differ in their molecular patterns. The basic division of the genus into two major clades had not previously been intimated on morphological grounds. Both major groups are thought to have survived in different glacial refugia and to have hybridized as a result of secondary contact. Several lines of evidence suggest the data is best explained by the presence of an extinct range of variation and a larger diversity of ancestral diploids in former times rather than by unsampled variation. Extinct diversity and extensive reticulation are thought to have largely obscured the species relationships. Our study illustrates how multigene sequences can be used to disentangle the evolutionary history of agamic complexes or similarly difficult datasets.
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Affiliation(s)
- Judith Fehrer
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, 25243 Průhonice, Czech Republic
| | - Karol Krak
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, 25243 Průhonice, Czech Republic
| | - Jindřich Chrtek
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, 25243 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University Prague, Benátská 2, 12801 Prague, Czech Republic
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Poczai P, Hyvönen J. Nuclear ribosomal spacer regions in plant phylogenetics: problems and prospects. Mol Biol Rep 2009; 37:1897-912. [PMID: 19626457 DOI: 10.1007/s11033-009-9630-3] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Accepted: 07/09/2009] [Indexed: 01/06/2023]
Affiliation(s)
- Péter Poczai
- Department of Plant Sciences and Biotechnology, Georgikon Faculty, University of Pannonia, Festetics 7, 8360, Keszthely, Hungary.
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Uzuhashi S, Kakishima M, Imazu M. Structure and organization of the rDNA intergenic spacer region in Pythium ultimum. MYCOSCIENCE 2009. [DOI: 10.1007/s10267-008-0473-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Kan XZ, Wang SS, Ding X, Wang XQ. Structural evolution of nrDNA ITS in Pinaceae and its phylogenetic implications. Mol Phylogenet Evol 2007; 44:765-77. [PMID: 17596969 DOI: 10.1016/j.ympev.2007.05.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Revised: 04/24/2007] [Accepted: 05/07/2007] [Indexed: 11/29/2022]
Abstract
Nuclear ribosomal DNA (nrDNA) has been considered as an important tool for inferring phylogenetic relationships at many taxonomic levels. In comparison with its fast concerted evolution in angiosperms, nrDNA is symbolized by slow concerted evolution and substantial ITS region length variation in gymnosperms, particularly in Pinaceae. Here we studied structure characteristics, including subrepeat composition, size, GC content and secondary structure, of nrDNA ITS regions of all Pinaceae genera. The results showed that the ITS regions of all taxa studied contained subrepeat units, ranging from 2 to 9 in number, and these units could be divided into two types, longer subrepeat (LSR) without the motif (5'-GGCCACCCTAGTC) and shorter subrepeat (SSR) with the motif. Phylogenetic analyses indicate that the homology of some SSRs still can be recognized, providing important informations for the evolutionary history of nrDNA ITS and phylogeny of Pinaceae. In particular, the adjacent tandem SSRs are not more closely related to one another than they are to remote SSRs in some genera, which may imply that multiple structure variations such as recombination have occurred in the ITS1 region of these groups. This study also found that GC content in the ITS1 region is relevant to its sequence length and subrepeat number, and could provide some phylogenetic information, especially supporting the close relationships among Picea, Pinus, and Cathaya. Moreover, several characteristics of the secondary structure of Pinaceae ITS1 were found as follows: (1) the structure is dominated by several extended hairpins; (2) the configuration complexity is positively correlated with subrepeat number; (3) paired subrepeats often partially overlap at the conserved motif (5'-GGCCACCCTAGTC), and form a long stem, while other subrepeats fold onto itself, leaving part of the conserved motif exposed in hairpin loops.
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Affiliation(s)
- Xian-Zhao Kan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, The Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, China
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