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Bruce G Baldwin - One of the best experts on this subject based on the ideXlab platform.
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phylogeny and ecological radiation of new world thistles cirsium cardueae compositae based on its and ets rdna sequence data
Molecular Ecology, 2002Co-Authors: Dean G Kelch, Bruce G BaldwinAbstract:Sequence data from a portion of the External Transcribed Spacer (ETS) and internal Transcribed Spacers (ITS-1 and ITS-2) of 18S-26S nuclear ribosomal DNA were used to resolve historical biogeography and ecology of true thistles (Cirsium, Cardueae, Compositae) in the New World. The 650 base-pair, 3' portion of the ETS examined here showed a level of variation across taxa similar to that of the ITS sequences included. A maximum-likelihood tree based on combined ETS and ITS sequences leads us to suggest that the New World species of true thistles constitute a major lineage, which in turn comprises several smaller lineages. A western North American lineage shows weak quartet-puzzling support, but includes a well-supported lineage of species endemic to the California Floristic Province. Comparisons of this Californian lineage with other neoendemic angiosperm groups of the region show that the Californian Cirsium lineage exhibits unusually high ecological diversity for a group displaying such low levels of rDNA sequence divergence across taxa. Similarly low levels of sequence divergence were found throughout the New World Cirsium lineage. These results indicate either that Cirsium underwent a rapid ecological radiation in North America, or that rDNA evolution in North American Cirsium has been highly conservative.
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structure molecular evolution and phylogenetic utility of the 5 region of the External Transcribed Spacer of 18s 26s rdna in lessingia compositae astereae
Molecular Phylogenetics and Evolution, 2002Co-Authors: Staci Markos, Bruce G BaldwinAbstract:Abstract The 18S-26S nuclear rDNA External Transcribed Spacer (ETS) has recently gained attention as a region that is valuable in phylogenetic analyses of angiosperms primarily because it can supplement nucleotide variation from the widely used and generally shorter internal Transcribed Spacers (ITS-1 and ITS-2) and thereby improve phylogenetic resolution and clade support in rDNA trees. Subrepeated ETS sequences (often occurring in the 5′ region) can, however, create a challenge for systematists interested in using ETS sequence data for phylogeny reconstruction. We sequenced the 5′ETS for members of Lessingia (Compositae, Astereae) and close relatives (26 taxa total) to characterize the subrepeat variation across a group of closely related plant lineages and to gain improved understanding of the structure, molecular evolution, and phylogenetic utility of the region. The 5′ETS region of Lessingia and relatives varied in length from ∼245 to 1009 bp due to the presence of a variable number of subrepeats (one to eight). We assessed homology of the subrepeats using phylogenetic analysis and concluded that only two of the subrepeats and a portion of a third (∼282 bp in total) were orthologous across Lessingia and could be aligned with confidence and included in further analyses. When the partial 5′ETS data were combined with 3′ETS and ITS data in phylogenetic analyses, no additional resolution of relationships among taxa was obtained beyond that found from analysis of 3′ETS + ITS sequences. Inferred patterns of concerted evolution indicate that homogenization is occurring at a faster rate in the 3′ETS and ITS regions than in the 5′ETS region. Additionally, homogenization appears to be acting within but not among subrepeats of the same rDNA array. We conclude that challenges in assessing subrepeat orthology across taxa greatly limit the utility of the 5′ETS region for phylogenetic analyses among species of Lessingia.
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unequal evolutionary rates between annual and perennial lineages of checker mallows sidalcea malvaceae evidence from 18s 26s rdna internal and External Transcribed Spacers
Molecular Biology and Evolution, 2001Co-Authors: Katarina Andreasen, Bruce G BaldwinAbstract:Heterogeneous DNA substitution rates were found in the 18S-26S nuclear ribosomal DNA internal Transcribed Spacer (ITS) and External Transcribed Spacer (ETS) regions of Sidalcea (Malvaceae), a putatively young genus of annuals and perennials. The majority of comparisons revealed that the annual species had significantly higher molecular evolutionary rates than the perennials, whereas rates were consistently homogenous between obligate annual species. These findings led us to conclude that generation time or possibly another biological factor distinguishing annuals and perennials has influenced rates of molecular evolution in SIDALCEA: The congruence of relative-rate test results across both Spacer regions reinforced the association between life history and rate of rDNA evolution across lineages of checker mallows. Evolutionary rate variation within perennials mainly involved three basally divergent lineages. The faster rate in one lineage, Sidalcea stipularis, compared with other perennials may be the result of genetic drift in the only known, small, population. The other two basally divergent lineages had slower evolutionary rates compared with the remaining perennials; possible explanations for these differences include rate-reducing effects of a suffrutescent (rather than herbaceous) habit and seed dormancy.
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higher level relationships and major lineages of lessingia compositae astereae based on nuclear rdna internal and External Transcribed Spacer its and ets sequences
Systematic Botany, 2001Co-Authors: Staci Markos, Bruce G BaldwinAbstract:Abstract The apparent recency of diversification of Californian Lessingia (Compositae, Astereae) makes the genus a particularly interesting group for evolutionary investigation. Here we focus on the major evolutionary lineages within Lessingia (sensu Lane 1992) and the higher-level relationships of the genus and presumed close relatives using sequence data from the 18S–26S nuclear ribosomal DNA (nrDNA) internal Transcribed Spacer (ITS) region and the 3’ end (561–563 bp) of the External Transcribed Spacer (ETS). We present new 3‘ETS primers that are useful across Astereae and examine the phylogenetic utility of the 3‘ETS in Lessingia and close relatives. In Lessingia, the 3‘ETS region appears to have evolved up to 1.4 times more rapidly by nucleotide substitution than has the ITS region. Our results show that data from the ETS greatly augments data from the ITS region; the combined data set yields the best resolved and best supported molecular trees for Lessingia. These topologies lead us to five conclusio...
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phylogenetic utility of the External Transcribed Spacer ets of 18s 26s rdna congruence of ets and its trees of calycadenia compositae
Molecular Phylogenetics and Evolution, 1998Co-Authors: Bruce G Baldwin, Staci MarkosAbstract:The 3' region of the External Transcribed Spacer (ETS) of 18S-26S nuclear ribosomal DNA was sequenced in 19 representatives of Calycadenia/Osmadenia and two outgroup species (Compositae) to assess its utility for phylogeny reconstruction compared to rDNA internal Transcribed Spacer (ITS) data. Universal primers based on plant, fungal, and animal sequences were designed to amplify the intergenic Spacer (IGS) and an angiosperm primer was constructed to sequence the 3' end of the ETS in members of tribe Heliantheae. Based on these sequences, an internal ETS primer useful across Heliantheae sensu lato was designed to amplify and sequence directly the 3' ETS region in the study taxa, which were the subjects of an earlier phylogenetic investigation based on ITS sequences. Size variation in the amplified ETS region varied across taxa of Heliantheae sensu lato from approximately 350 to 700 bp, in part attributable to an approximately 200-bp tandem duplication in a common ancestor of Calycadenia/Osmadenia. Phylogenetic analysis of the 200-bp subrepeats and examination of apomorphic changes in the duplicated region demonstrate that the subrepeats in Calycadenia/Osmadenia have evolved divergently. Phylogenetic analyses of the entire amplified ETS region yielded a highly resolved strict consensus tree that is nearly identical in topology to the ITS tree, with strong bootstrap and decay support on most branches. Parsimony analyses of combined ETS and ITS data yielded a strict consensus tree that is better resolved and generally better supported than trees based on either data set analyzed separately. We calculated an approximately 1.3- to 2.4-fold higher rate of sequence evolution by nucleotide substitution in the ETS region studied than in ITS-1 + ITS-2. A similar disparity in the proportion of variable (1.3 ETS:1 ITS) and potentially informative (1.5 ETS:1 ITS) sites was observed for the ingroup. Levels of homoplasy are similar in the ETS and ITS data. We conclude that the ETS holds great promise for augmenting ITS data for phylogenetic studies of young lineages.
David Tollervey - One of the best experts on this subject based on the ideXlab platform.
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the role of the 3 External Transcribed Spacer in yeast pre rrna processing
Journal of Molecular Biology, 1998Co-Authors: Christine Allmang, David TollerveyAbstract:We have undertaken a deletion analysis of the 3' External Transcribed Spacer (3' ETS) in the pre-rRNA of Saccharomyces cerevisiae. A stem loop structure immediately 3' to the 25 S rRNA region is necessary and sufficient for processing of the 3' ETS. This is believed to be by cotranscriptional cleavage by Rnt1p, the yeast homologue of RNase III. In addition, this stem-loop is required for cleavage of site A3 by RNase MRP and for processing at site B1L, in the 3' region of ITS1. Processing at an upstream site in ITS1, site A2, and at sites in the 5' External Transcribed Spacer are not affected, even by complete deletion of the 3' ETS. We conclude that processing in the 3' ETS and in ITS1 is coupled. This would constitute a quality control that prevents synthesis of the 5. 8 S rRNA and 5' end maturation of the 25 S rRNA in transcripts which are incomplete due to premature transcription termination.
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dob1p mtr4p is a putative atp dependent rna helicase required for the 3 end formation of 5 8s rrna in saccharomyces cerevisiae
The EMBO Journal, 1998Co-Authors: Jesus De La Cruz, David Tollervey, Dieter Kressler, Patrick LinderAbstract:The temperature-sensitive mutation, dob1-1, was identified in a screen for dependence on overexpression of the yeast translation initiation factor eIF4B (Tif3p). Dob1p is an essential putative ATP-dependent RNA helicase. Polysome analyses revealed an under accumulation of 60S ribosomal subunits in the dob1-1 mutant. Pulse-chase labelling of pre-rRNA showed that this was due to a defect in the synthesis of the 5.8S and 25S rRNAs. Northern and primer extension analyses in the dob1-1 mutant, or in a strain genetically depleted of Dob1p, revealed a specific inhibition of the 3' processing of the 5.8S rRNA from its 7S precursor. This processing recently has been attributed to the activity of the exosome, a complex of 3'-->5' exonucleases that includes Rrp4p. In vivo depletion of Dob1p also inhibits degradation of the 5' External Transcribed Spacer region of the pre-rRNA. A similar phenotype was observed in rrp4 mutant strains and, moreover, the dob1-1 and rrp4-1 mutations show a strong synergistic growth inhibition. We propose that Dob1p functions as a cofactor for the exosome complex that unwinds secondary structures in the pre-rRNA that otherwise block the progression of the 3'-->5' exonucleases.
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base pairing between u3 and the pre ribosomal rna is required for 18s rrna synthesis
The EMBO Journal, 1995Co-Authors: Monica Beltrame, David TollerveyAbstract:Abstract The nucleolus, the site of pre-ribosomal RNA (pre-rRNA) synthesis and processing in eukaryotic cells, contains a number of small nucleolar RNAs (snoRNAs). Yeast U3 snoRNA is required for the processing of 18S rRNA from larger precursors and contains a region complementary to the pre-rRNA. Substitution mutations in the pre-rRNA which disrupt this base pairing potential are lethal and prevent synthesis of 18S rRNA. These mutant pre-rRNAs show defects in processing which closely resemble the effects of genetic depletion of components of the U3 snoRNP. Co-expression of U3 snoRNAs which carry compensatory mutations allows the mutant pre-rRNAs to support viability and synthesize 18S rRNA at high levels. Pre-rRNA processing steps which are blocked by the External Transcribed Spacer region mutations are largely restored by expression of the compensatory U3 mutants. Pre-rRNA processing therefore requires direct base pairing between snoRNA and the substrate. Base pairing with the substrate is thus a common feature of small RNAs involved in mRNA and rRNA maturation.
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mutational analysis of an essential binding site for the u3 snorna in the 5 External Transcribed Spacer of yeast pre rrna
Nucleic Acids Research, 1994Co-Authors: Monica Beltrame, Yves Henry, David TollerveyAbstract:The small nucleolar RNA U3 is essential for viability in yeast. We have previously shown that U3 can be cross-linked in vivo to the pre-rRNA in the 5' External Transcribed Spacer (ETS), at +470. This ETS region contains 10 nucleotides of perfect complementarity to U3. In a genetic background where the mutated rDNA is the only Transcribed rDNA repeat, the deletion of the 10 nt complementary to U3 is lethal. Cells lacking the U3 complementary sequence in pre-rRNA fail to accumulate 18S rRNA: pre-rRNA processing is inhibited at sites A0 in the 5' ETS, A1 at the 5' end of 18S rRNA and A2 in ITS1. We show here that effects on processing at site A0 are specific for U3 and its associated proteins and are not seen on depletion of other snoRNP components. The deletion of the sequence complementary to U3 in the ETS therefore mimics all the known effects of the depletion of U3 in trans. This indicates that we have identified an essential U3 binding site on pre-rRNA, required in cis for the maturation of 18S rRNA.
Ross N Nazar - One of the best experts on this subject based on the ideXlab platform.
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rac protein directs the complete removal of the 3 External Transcribed Spacer by the pac1 nuclease
Molecular Cell, 2002Co-Authors: Krasimir Spasov, Liliana I Perdomo, Eugeni Evakine, Ross N NazarAbstract:Abstract In Schizosaccharomyces pombe , interdependency in rRNA processing is mediated by a large protein complex (RAC) which contains independent binding sites for each of the Transcribed Spacers. The RAC complex exhibits no nuclease activity but dramatically alters the efficiency and specificity of the Pac1 nuclease, leading to the complete removal of the 3′ETS. Furthermore, the affinity of RAC protein for mutant 3′ETS correlates closely with in vivo effects on rRNA processing, and changes which disrupt RAC protein binding also inhibit Pac1 nuclease cleavage at the 3′ end of the 25S rRNA sequence. The observations indicate that, in the presence of the RAC protein/3′ETS complex, cleavage by the RNase III-like homolog is not restricted to the known intermediate sites but also is directed at the 3′ end of the 25S rRNA.
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essential structural features in the schizosaccharomyces pombe pre rrna 5 External Transcribed Spacer
Journal of Molecular Biology, 1999Co-Authors: Robert V Intine, Liam Good, Ross N NazarAbstract:Abstract The proximal region in the 5′ External Transcribed Spacer (5′ETS) of the genes encoding ribosomal RNAs in Schizosaccharomyces pombe was examined with respect to structural features which underlie rRNA maturation. Computer analyses and partial digestion with nuclease probes indicate a crucifix-like structure composed primarily of three extended hairpins which are more highly ordered than previously proposed in Saccharomyces cerevisiae. A re-evaluation of the same region in S. cerevisiae indicates a conserved core structure, including the U3 snoRNA binding site within this higher-order structure. The sequences encoding the individual hairpins were deleted by PCR-mediated mutagenesis and the mutant rDNAs were expressed in vivo to determine the effect of these features on rRNA maturation. Quantitative hybridization analyses indicate that the first hairpin only has modest effects on 18 S rRNA maturation, but the other two regions are critical and no mature 18 S rRNA was observed. When smaller changes were systematically introduced into the critical regions, strong correlations were observed with known or putative events in rRNA maturation. Changes associated with an intermediate cleavage site in helix II and with the putative U3 snoRNA binding site were again critical to 18 S rRNA production. In each case, the effects were sequence dependent and not simply the result of disrupted structure. Further analyses of the 5.8 S rRNA indicate that the large ribosomal subunit RNA can be properly processed in each case but the efficiency is reduced by as much as 60 %, an observation which provides new evidence of interdependency in the maturation process. The results illustrate that rRNA processing is more critically dependent on the 5′ETS than previously believed.
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structural features in the 3 External Transcribed Spacer affecting intragenic processing of yeast rrna
Journal of Molecular Biology, 1997Co-Authors: John Hitchen, Yuri F Melekhovets, Evgueni A Ivakine, Atanas I Lalev, Ross N NazarAbstract:A highly conserved extended hairpin structure in the 3' External Transcribed Spacer (3' ETS) region of nascent eukaryotic rRNA transcripts is essential for the maturation of the large ribosomal subunit RNAs (5.8 S and 25 to 28 S rRNAs). Systematic changes were introduced into this structure by PCR-mediated mutagenesis and the mutant rDNAs were expressed in vivo to determine the structural features that are essential for rRNA maturation. Changes in the lower half of the stem or the large loop at the end had little or no effect on the maturation of either the 5.8 S or 25 S rRNA, but changes that disrupted secondary structure in the upper half of this stem had equal and dramatic effects on both RNAs. When the RNA stem was incubated with a cellular protein extract, gel retardation studies indicated that the stem forms a ribonucleoprotein complex, and a comparison with mutant RNA indicated that protein binding could be compromised by changes that were critical for rRNA maturation. Sequence comparisons with other Spacer regions as well as snRNAs reveal some structural analogy, which, when taken together with the mutational studies, raise the possibility that this hairpin functions during RNA processing in a manner that may be analogous with that of free snRNPs.
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intragenic processing in yeast rrna is dependent on the 3 External Transcribed Spacer
Journal of Molecular Biology, 1994Co-Authors: Yuri F Melekhovets, Liam Good, Sherif Abou Elela, Ross N NazarAbstract:Abstract The nucleotide sequence of the 3′ External Transcribed Spacer (3′ ETS) region in Schizosaccharomyces pombe rDNA was determined to define structural features which mediate the termination of RNA transcription and subsequent rRNA maturation. S1 nuclease protection studies suggest three alternative termination sites and four cleavage sites in the processing of the 3′ ETS sequence. Each of the termination sites precedes a "Sal box"-like sequence which has been demonstrated to mediate the termination of rRNA transcription in mammalian cells. A highly conserved extended hairpin structure in the ETS sequence was deleted by PCR-mediated mutagenesis and the mutant rDNA was expressed in vivo to determine its role in rRNA maturation. Despite an efficient expression of the mutant gene, mature 5′8 S or 25 S rRNA was not observe. Labelling kinetics and S1 nuclease protection analyses indicate that the deletion not only fully inhibits the removal of the 3′ ETS but also fully inhibits the processive excision of the second internal Transcribed Spacer (ITS2). Instead, a relatively stable 27 S nRNA precursor remains easily detectable in the whole cell RNA population. The results demonstrate a critical dependence of ITS processing on the 3′ ETS raising the possibility that these sequences interact in a common processing domain.
Randal C Linder - One of the best experts on this subject based on the ideXlab platform.
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HIGH-RESOLUTION PHYLOGENY FOR HELIANTHUS (ASTERACEAE) USING THE 18S-26S RIBOSOMAL DNA External Transcribed Spacer 1
2015Co-Authors: Ruth E. Timme, Beryl B Simpson, Randal C LinderAbstract:The sunflower genus, Helianthus, is recognized widely for the cultivated sunflower H. annuus and scientifically as a model organism for studying diploid and polyploid hybrid speciation, introgression, and genetic architecture. A resolved phylogeny for the genus is essential for the advancement of these scientific areas. In the past, phylogenetic relationships of the perennial species and polyploid hybrids have been particularly difficult to resolve. Using the External Transcribed Spacer region of the nuclear 18S-26S rDNA region, we reveal for the first time a highly resolved gene tree for Helianthus. Phylogenetic analysis allowed the determination of a monophyletic annual H. sect. Helianthus, a two-lineage polyphyletic H. sect. Ciliares, and the monotypic H. sect. Agrestis, all of which were nested within a large perennial and polyphyletic H. sect. Divaricati. The distribution of perennial polyploids and known annual diploid hybrids on this phylogeny suggested multiple independent hybrid speciation events that gave rise to at least four polyploids and three diploid hybrids. Also provided by this phylogeny was evidence for homoploid hybrid speciation outside H. sect. Helianthus. Finally, previous hypotheses about the secondary chemistry in the genus were tested in a phylogenetic framework to obtain a better understanding of the evolution of these compounds in Helianthus. Key words: Asteraceae; ETS; Helianthus; hybrid; phylogeny; polyploidy; reticulate evolution; rDNA; secondary chemistry. Given the economic and cultural importance of the common sunflower, Helianthus annuus, there has been broad interest in the genus in which it evolved. Helianthus also has become a
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high resolution phylogeny for helianthus asteraceae using the 18s 26s ribosomal dna External Transcribed Spacer
American Journal of Botany, 2007Co-Authors: Ruth E. Timme, Beryl B Simpson, Randal C LinderAbstract:The sunflower genus, Helianthus, is recognized widely for the cultivated sunflower H. annuus and scientifically as a model organism for studying diploid and polyploid hybrid speciation, introgression, and genetic architecture. A resolved phylogeny for the genus is essential for the advancement of these scientific areas. In the past, phylogenetic relationships of the perennial species and polyploid hybrids have been particularly difficult to resolve. Using the External Transcribed Spacer region of the nuclear 18S 26S rDNA region, we reveal for the first time a highly resolved gene tree for Helianthus. Phylogenetic analysis allowed the determination of a monophyletic annual H. sect. Helianthus, a two-lineage polyphyletic H. sect. Ciliares, and the monotypic H. sect. Agrestis, all of which were nested within a large perennial and polyphyletic H. sect. Divaricati. The distribution of perennial polyploids and known annual diploid hybrids on this phylogeny suggested multiple independent hybrid speciation events that gave rise to at least four polyploids and three diploid hybrids. Also provided by this phylogeny was evidence for homoploid hybrid speciation outside H. sect. Helianthus. Finally, previous hypotheses about the secondary chemistry in the genus were tested in a phylogenetic framework to obtain a better understanding of the evolution of these compounds in Helianthus.
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the complete External Transcribed Spacer of 18s 26s rdna amplification and phylogenetic utility at low taxonomic levels in asteraceae and closely allied families
Molecular Phylogenetics and Evolution, 2000Co-Authors: Randal C Linder, Leslie R Goertzen, Brian Vanden Heuvel, Javier Franciscoortega, Robert K JansenAbstract:For molecular phylogenetic reconstruction of some intrageneric groups of plants, a DNA region is needed that evolves more rapidly than the internal Transcribed Spacer (ITS) of the 18S-26S nuclear ribosomal DNA (nrDNA) repeat. If the region identified is nuclear, it would also be desirable for it to undergo rapid concerted evolution to eliminate problems with coalescence. The External Transcribed Spacer (ETS) of the nrDNA repeat has shown promise for intrageneric phylogenetic reconstruction, but only the 3' end of the region has been utilized for phylogenetic reconstruction and "universal" primers for PCR amplification have been elusive. We present a method for reliably amplifying and sequencing the entire ETS throughout Asteraceae and some closely allied families. We also show that the ETS is more variable and phylogenetically informative than the ITS in three disparate genera of Asteraceae-Argyranthemum (tribe Anthemideae), Asteriscus (tribe Inuleae), and Helianthus (tribe Heliantheae). The full ETS was amplified using a primer (ETS1f) within the intergenic Spacer in combination with a primer (18S-2L) in the 5' end of the highly conserved 18S gene. ETS1f was designed to correspond to a highly conserved region found in Helianthus and Crepis, which are in separate subfamilies of Asteraceae. ETS1f/18S-2L primed in all of the tribes of Asteraceae as well as exemplar taxa from Campanulaceae, Goodeniaceae, and Calyceraceae. For both Argyranthemum and Asteriscus, we were able to directly sequence the ETS PCR products when a single band was produced. When multiple bands were produced, we gel-purified and occasionally cloned the band of interest before sequencing. Although PCR produced single bands for Helianthus species, it was necessary to clone Helianthus amplifications prior to sequencing due to multiple intragenomic ETS repeat types. Alignment of ETS sequences for Argyranthemum and Asteriscus was straightforward and unambiguous despite some subrepeat structure in the 5' end. For Helianthus, different numbers of large tandem subrepeats in different species required analysis of the orthology of the subrepeats prior to alignment. In all three genera, the ETS provided more informative variation for phylogenetic reconstruction and allowed better resolution of relationships than the ITS. Although cloned sequences from Helianthus differed, intragenomic clones consistently formed clades. This result indicated that concerted evolution was proceeding rapidly enough in ETS that species-specific phylogenetic signal was retained. It should be now be possible to use the entire ETS for phylogenetic reconstruction of recently diverged lineages in Asteraceae and at least three other families (approximately 26,000 species or about 8% of all angiosperms).
Vera Hemleben - One of the best experts on this subject based on the ideXlab platform.
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Molecular evolution of rDNA External Transcribed Spacer and phylogeny of sect. Petota (genus Solanum).
Molecular phylogenetics and evolution, 2003Co-Authors: Roman A. Volkov, Nataliya Y. Komarova, Irina I. Panchuk, Vera HemlebenAbstract:Abstract The 5 ′ External Transcribed Spacer (ETS) region of ribosomal DNA of 30 species of Solanum sect. Petota and the European Solanum dulcamara were compared. Two structural elements can be distinguished in the ETS: (i) a variable region (VR), demonstrating significant structural rearrangements and (ii) a conservative region (CR), evolving mainly by base substitutions. In VR, a conservative element (CE) with similarity to the ETS of distantly related Nicotiana is present. The ancestral organization of ETS (variant A) was found for non-tuber-bearing species of ser. Etuberosa , tuber-bearing wild potatoes of Central American ser. Bulbocastana , Pinnatisecta , and Polyadenia and S. dulcamara . Duplication of CE took place in the ETS of species from ser. Commersoniana and Circaeifolia (variant B). South American diploids and Mexican polyploids from superser. Rotata also possess two CE, and additionally two duplications around CE1 are present in VR (variant C). Three major lineages could be distinguished: non-tuber-bearing species of ser. Etuberosa , tuber-bearing Central American diploids and all South American species radiated from a common ancestor at early stages of evolution, indicating a South American origin of the tuber-bearing species. Later, Central and South American diploids evolved further as independent lineages. South American species form a monophyletic group composed of series with both stellata and rotata flower morphology. Solanum commersonii represents a sister taxon for all rotata species, whereas ser. Circaeifolia diverged earlier. Two main groups, C1 and C2, may be distinguished for species possessing ETS variant C. C1 contains ser. Megistacroloba , Conicibaccata , Maglia , and Acaulia , whereas all diploids of ser. Tuberosa are combined into C2. A closer relationship of Solanum chacoense (ser. Yungasensa ) to the C2 group was found. The origin of polyploid species Solanum maglia , Solanum acaule , Solanum tuberosum , Solanum iopetalum , and Solanum demissum is discussed.
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nuclear proteins interact with rna polymerase i promoter and repeated elements of the 5 External Transcribed Spacer of the rdna of cucumber in a single stranded stage
Plant Molecular Biology, 1993Co-Authors: Ulrike Zentgraf, Vera HemlebenAbstract:Directly repeated elements have been characterized downstream of the transcription initiation site (TIS) in the 5′ External Transcribed Spacer (5′ ETS) of the rRNA genes of cucumber (Cucumis sativus). In order to show that these repeated elements are also involved in transcriptional regulation processes of RNA polymerase I while being single-stranded during transcription, DNA-protein binding assays were performed with synthetic oligonucleotides prepared from the promoter region as well as from the repeated elements. The single-stranded DNA of the upstream binding element (from −164 to −105), the core promoter (from −41 to +16) and a loop-forming sequence (LRE) of the repeated elements interact with the same nuclear proteins whereas another region of the repeated elements (XRE) cooperates with a different nuclear protein. Remarkably, both complementary strands show identical protein binding.
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complex formation of nuclear proteins with the rna polymerase i promoter and repeated elements in the External Transcribed Spacer of cucumis sativus ribosomal dna
Nucleic Acids Research, 1992Co-Authors: Ulrike Zentgraf, Vera HemlebenAbstract:Complex repetitive structures are located downstream of the transcription initiation site in the intergenic Spacer (IGS) of the rRNA genes in Cucumis sativus (cucumber). In order to show that these repetitive elements of the 5'External Transcribed Spacer (ETS) are probably involved in transcriptional regulation as protein binding sites DNA-protein binding assays were carried out. The same proteins that recognize two binding sites in the promoter region analysed (upstream binding element between -164 and -105, and core promoter between -41 and +16) show binding affinity to the complex structures of the 5'External Transcribed Spacer. These proteins also seem to interact with the single strands of the respective DNA regions suggesting an effect on transcriptional regulation while the DNA is Transcribed and, therefore, is single-stranded. Three proteins were isolated by affinity column chromatography; these proteins turned out to be much smaller (16, 22, and 24 kDa, respectively) than promoter and enhancer binding proteins in animal systems. Additionally, a 70-kDa protein could be characterized cooperating with a small segment of the repeated elements but not with the promoter.
