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Austen R. D. Ganley - One of the best experts on this subject based on the ideXlab platform.
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monitoring the rate and dynamics of Concerted Evolution in the ribosomal dna repeats of saccharomyces cerevisiae using experimental Evolution
Molecular Biology and Evolution, 2011Co-Authors: Austen R. D. Ganley, Takehiko KobayashiAbstract:Concerted Evolution describes the unusual Evolutionary pattern exhibited by certain repetitive sequences, whereby all the repeats are maintained in the genome with very similar sequences but differ between related species. The pattern of Concerted Evolution is thought to result from continual turnover of repeats by recombination, a process known as homogenization. Approaches to studying Concerted Evolution have largely been observational because of difficulties investigating repeat Evolution in an experimental setting with large arrays of identical repeats. Here, we establish an experimental Evolution approach to look at the rate and dynamics of Concerted Evolution in the ribosomal DNA (rDNA) repeats. A small targeted mutation was made in the spacer of a single rDNA unit in Saccharomyces cerevisiae so we could monitor the fate of this unit without the need for a selectable marker. The rate of loss of this single unit was determined, and the frequency of duplication was also estimated. The results show that duplication and deletion events occur at similar rates and are very common: An rDNA unit may be gained or lost as frequently as once every cell division. Investigation of the spatial dynamics of rDNA turnover showed that when the tagged repeat unit was duplicated, the copy predominantly, but not exclusively, ended up near to the tagged repeat. This suggests that variants in the rDNA spread in a semiclustered fashion. Surprisingly, large deletions that remove a significant fraction of total rDNA repeats were frequently found. We propose these large deletions are a driving force of Concerted Evolution, acting to increase homogenization efficiency over-and-above that afforded by turnover of individual rDNA units. Thus, the results presented here enhance our understanding of Concerted Evolution by offering insights into both the spatial and temporal dynamics of the homogenization process and suggest an important new aspect in our understanding of Concerted Evolution.
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highly efficient Concerted Evolution in the ribosomal dna repeats total rdna repeat variation revealed by whole genome shotgun sequence data
Genome Research, 2007Co-Authors: Austen R. D. Ganley, Takehiko KobayashiAbstract:Repeat families within genomes are often maintained with similar sequences. Traditionally, this has been explained by Concerted Evolution, where repeats in an array evolve "in concert" with the same sequence via continual turnover of repeats by recombination. Another form of Evolution, birth-and-death Evolution, can also explain this pattern, although in this case selection is the critical force maintaining the repeats. The level of intragenomic variation is the key difference between these two forms of Evolution. The prohibitive size and repetitive nature of large repeat arrays have made determination of the absolute level of intragenomic repeat variability difficult, thus there is little evidence to support Concerted Evolution over birth-and-death Evolution for many large repeat arrays. Here we use whole-genome shotgun sequence data from the genome projects of five fungal species to reveal absolute levels of sequence variation within the ribosomal RNA gene repeats (rDNA). The level of sequence variation is remarkably low. Furthermore, the polymorphisms that are detected are not functionally constrained and seem to exist beneath the level of selection. These results suggest the rDNA is evolving via Concerted Evolution. Comparisons with a repeat array undergoing birth-and-death Evolution provide a clear contrast in the level of repeat array variation between these two forms of Evolution, confirming that the rDNA indeed does evolve via Concerted Evolution. These low levels of intra-genomic variation are consistent with a model of Concerted Evolution in which homogenization is very rapid and efficiently maintains highly similar repeat arrays.
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Concerted Evolution in the ribosomal rna genes of an epichloe endophyte hybrid comparison between tandemly arranged rdna and dispersed 5s rrn genes
Fungal Genetics and Biology, 2002Co-Authors: Austen R. D. Ganley, Barry ScottAbstract:We examined ribosomal RNA Concerted Evolution in an Epichloe endophyte interspecific hybrid (Lp1) and its progenitors (Lp5 and E8). We show that the 5S rrn genes are organized as dispersed copies. Cloned 5S gene sequences revealed two subfamilies exhibiting 12% sequence divergence, with substitutions forming coevolving pairs that maintain secondary structure and presumably function. Observed sequence patterns are not fully consistent with either Concerted or classical Evolution. The 5S rrn genes are syntenic with the tandemly arranged rDNA genes, despite residing outside the rDNA arrays. We also examined rDNA Concerted Evolution. Lp1 has rDNA sequence from only one progenitor and contains multiple rDNA arrays. Using 5S rrn genes as chromosomal markers, we propose that interlocus homogenization has replaced all Lp5 rDNA sequence with E8 sequence in the hybrid. This interlocus homogenization appears to have been rapid and efficient and is the first demonstration of hybrid interlocus homogenization in the Fungi.
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Extraordinary Ribosomal Spacer Length Heterogeneity in a Neotyphodium Endophyte Hybrid: Implications for Concerted Evolution
Genetics, 1998Co-Authors: Austen R. D. Ganley, Barry ScottAbstract:An extraordinary level of length heterogeneity was found in the ribosomal DNA (rDNA) of an asexual hybrid Neotyphodium grass endophyte, isolate Lp1. This hybrid Neotyphodium endophyte is an interspecific hybrid between two grass endophytes, Neotyphodium lolii, and a sexual form, Epichloe typhina, and the length heterogeneity was not found in either of these progenitor species. The length heterogeneity in the hybrid is localized to the intergenic spacer (IGS) and is the result of copy-number variation of a tandemly repeated subrepeat class within the IGS, the 111-/119-bp subrepeats. Copy number variation of this subrepeat class appears to be a consequence of mitotic unequal crossing over that occurs between these subrepeats. This implies that unequal crossing over plays a role in the Concerted Evolution of the whole rDNA. Changes in the pattern of IGS length variants occurred in just two rounds of single-spore purification. Analysis of the IGS length heterogeneity revealed features that are unexpected in a simple model of unequal crossing over. Potential refinements of the molecular details of unequal crossing over are presented, and we also discuss evidence for a combination of homogenization mechanisms that drive the Concerted Evolution of the Lp1 rDNA.
Daiqing Liao - One of the best experts on this subject based on the ideXlab platform.
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gene conversion drives within genic sequences Concerted Evolution of ribosomal rna genes in bacteria and archaea
Journal of Molecular Evolution, 2000Co-Authors: Daiqing LiaoAbstract:Multiple copies of a given ribosomal RNA gene family undergo Concerted Evolution such that sequences of all gene copies are virtually identical within a species although they diverge normally between species. In eukaryotes, gene conversion and unequal crossing over are the proposed mechanisms for Concerted Evolution of tandemly repeated sequences, whereas dispersed genes are homogenized by gene conversion. However, the homogenization mechanisms for multiple-copy, normally dispersed, prokaryotic rRNA genes are not well understood. Here we compared the sequences of multiple paralogous rRNA genes within a genome in 12 prokaryotic organisms that have multiple copies of the rRNA genes. Within a genome, putative sequence conversion tracts were found throughout the entire length of each individual rRNA genes and their immediate flanks. Individual conversion events convert only a short sequence tract, and the conversion partners can be any paralogous genes within the genome. Interestingly, the genic sequences undergo much slower divergence than their flanking sequences. Moreover, genomic context and operon organization do not affect rRNA gene homogenization. Thus, gene conversion underlies Concerted Evolution of bacterial rRNA genes, which normally occurs within genic sequences, and homogenization of flanking regions may result from co-conversion with the genic sequence.
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Concerted Evolution of the tandem array encoding primate u2 snrna the rnu2 locus is accompanied by dramatic remodeling of the junctions with flanking chromosomal sequences
The EMBO Journal, 1999Co-Authors: Thomas Pavelitz, Daiqing Liao, Alan M WeinerAbstract:The genes encoding primate U2 snRNA are organized as a nearly perfect tandem array (the RNU2 locus) that has been evolving Concertedly for >35 Myr since the divergence of baboons and humans. Thus the repeat units of the tandem array are essentially identical within each species, but differ between species. Homogeneity is maintained because any change in one repeat unit is purged from the array or fixed in all other repeats. Intriguingly, the cytological location of RNU2 has remained unchanged despite Concerted Evolution of the tandem array. We had found previously that junction sequences between the U2 tandem array and flanking DNA were subject to remodeling over a region of 200-300 bp during the past 5 Myr in the hominid lineage. Here we show that the junctions between the U2 tandem array and flanking DNA have undergone dramatic rearrangements over a region of 1 to >10 kbp in the 35 Myr since divergence of the Old World Monkey and hominid lineages. We argue that these rearrangements reflect the high level of genetic activity required to sustain Concerted Evolution, and propose a model to explain why maintenance of homogeneity within a tandemly repeated multigene family would lead to junctional diversity.
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Concerted Evolution molecular mechanism and biological implications
American Journal of Human Genetics, 1999Co-Authors: Daiqing LiaoAbstract:A surprisingly large fraction of the eukaryotic genome is repetitive. More than one third of the human genome consists of interspersed repetitive DNA, and tandemly repeated DNA sequences may occupy as much as 10% of the human genome. The majority of the repetitive sequences are nongenic; the rest encode multigene families. The genomic organization of repetitive DNA sequences takes different forms: these repetitive sequences either disperse throughout the genome, as with short interspersed sequences (SINEs), long interspersed sequences (LINEs), and transposable elements, or, like tRNA genes and human histone genes, they may cluster in one or a few chromosomal regions.
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Concerted Evolution of the tandemly repeated genes encoding human u2 snrna the rnu2 locus involves rapid intrachromosomal homogenization and rare interchromosomal gene conversion
The EMBO Journal, 1997Co-Authors: Daiqing Liao, Thomas Pavelitz, Judith R Kidd, Kenneth K Kidd, Alan M WeinerAbstract:We have surveyed the tandemly repeated genes encoding U2 snRNA in a diverse panel of humans. We found only two polymorphisms within the U2 repeat unit: a SacI polymorphism (alleles SacI+ or SacI-) and a CT microsatellite polymorphism (alleles CT+ or CT-). Surprisingly, individual U2 tandem arrays are entirely SacI+ or SacI-, and entirely CT+ or CT-, although the SacI and CT alleles can occur in any combination. We also found that polymorphisms in the left and right junction regions flanking the tandem array fall into only two haplotypes (JL+ and JL-, JR+ and JR-). Most surprisingly, JL+ is always associated with JR+, and JL- with JR-. Thus individual U2 arrays do not exchange flanking markers, despite independent assortment and subsequent homogenization of the SacI and CT alleles within the U2 repeat units. We propose that the primary driving force for Concerted Evolution of the tandem U2 genes is intrachromosomal homogenization; interchromosomal genetic exchanges are much rarer, and reciprocal nonsister chromatid exchange apparently does not occur. Thus Concerted Evolution of the U2 tandem array occurs in situ along a chromosome lineage, and linkage disequilibrium between sequences flanking the U2 array may persist for long periods of time.
Takehiko Kobayashi - One of the best experts on this subject based on the ideXlab platform.
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monitoring the rate and dynamics of Concerted Evolution in the ribosomal dna repeats of saccharomyces cerevisiae using experimental Evolution
Molecular Biology and Evolution, 2011Co-Authors: Austen R. D. Ganley, Takehiko KobayashiAbstract:Concerted Evolution describes the unusual Evolutionary pattern exhibited by certain repetitive sequences, whereby all the repeats are maintained in the genome with very similar sequences but differ between related species. The pattern of Concerted Evolution is thought to result from continual turnover of repeats by recombination, a process known as homogenization. Approaches to studying Concerted Evolution have largely been observational because of difficulties investigating repeat Evolution in an experimental setting with large arrays of identical repeats. Here, we establish an experimental Evolution approach to look at the rate and dynamics of Concerted Evolution in the ribosomal DNA (rDNA) repeats. A small targeted mutation was made in the spacer of a single rDNA unit in Saccharomyces cerevisiae so we could monitor the fate of this unit without the need for a selectable marker. The rate of loss of this single unit was determined, and the frequency of duplication was also estimated. The results show that duplication and deletion events occur at similar rates and are very common: An rDNA unit may be gained or lost as frequently as once every cell division. Investigation of the spatial dynamics of rDNA turnover showed that when the tagged repeat unit was duplicated, the copy predominantly, but not exclusively, ended up near to the tagged repeat. This suggests that variants in the rDNA spread in a semiclustered fashion. Surprisingly, large deletions that remove a significant fraction of total rDNA repeats were frequently found. We propose these large deletions are a driving force of Concerted Evolution, acting to increase homogenization efficiency over-and-above that afforded by turnover of individual rDNA units. Thus, the results presented here enhance our understanding of Concerted Evolution by offering insights into both the spatial and temporal dynamics of the homogenization process and suggest an important new aspect in our understanding of Concerted Evolution.
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highly efficient Concerted Evolution in the ribosomal dna repeats total rdna repeat variation revealed by whole genome shotgun sequence data
Genome Research, 2007Co-Authors: Austen R. D. Ganley, Takehiko KobayashiAbstract:Repeat families within genomes are often maintained with similar sequences. Traditionally, this has been explained by Concerted Evolution, where repeats in an array evolve "in concert" with the same sequence via continual turnover of repeats by recombination. Another form of Evolution, birth-and-death Evolution, can also explain this pattern, although in this case selection is the critical force maintaining the repeats. The level of intragenomic variation is the key difference between these two forms of Evolution. The prohibitive size and repetitive nature of large repeat arrays have made determination of the absolute level of intragenomic repeat variability difficult, thus there is little evidence to support Concerted Evolution over birth-and-death Evolution for many large repeat arrays. Here we use whole-genome shotgun sequence data from the genome projects of five fungal species to reveal absolute levels of sequence variation within the ribosomal RNA gene repeats (rDNA). The level of sequence variation is remarkably low. Furthermore, the polymorphisms that are detected are not functionally constrained and seem to exist beneath the level of selection. These results suggest the rDNA is evolving via Concerted Evolution. Comparisons with a repeat array undergoing birth-and-death Evolution provide a clear contrast in the level of repeat array variation between these two forms of Evolution, confirming that the rDNA indeed does evolve via Concerted Evolution. These low levels of intra-genomic variation are consistent with a model of Concerted Evolution in which homogenization is very rapid and efficiently maintains highly similar repeat arrays.
Paul F Alewood - One of the best experts on this subject based on the ideXlab platform.
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PHAB toxins: a unique family of predatory sea anemone toxins evolving via intra-gene Concerted Evolution defines a new peptide fold
Cellular and Molecular Life Sciences, 2018Co-Authors: Bruno Madio, Yanni K. Y. Chin, Brett R. Hamilton, Sónia Troeira Henriques, Ben Cristofori-armstrong, Zoltan Dekan, Berin A. Boughton, Steve Peigneur, Jennifer J. Smith, Paul F AlewoodAbstract:Sea anemone venoms have long been recognized as a rich source of peptides with interesting pharmacological and structural properties, but they still contain many uncharacterized bioactive compounds. Here we report the discovery, three-dimensional structure, activity, tissue localization, and putative function of a novel sea anemone peptide toxin that constitutes a new, sixth type of voltage-gated potassium channel (K_V) toxin from sea anemones. Comprised of just 17 residues, κ-actitoxin-Ate1a (Ate1a) is the shortest sea anemone toxin reported to date, and it adopts a novel three-dimensional structure that we have named the Proline-Hinged Asymmetric β-hairpin (PHAB) fold. Mass spectrometry imaging and bioassays suggest that Ate1a serves a primarily predatory function by immobilising prey, and we show this is achieved through inhibition of Shaker-type K_V channels. Ate1a is encoded as a multi-domain precursor protein that yields multiple identical mature peptides, which likely evolved by multiple domain duplication events in an actinioidean ancestor. Despite this ancient Evolutionary history, the PHAB-encoding gene family exhibits remarkable sequence conservation in the mature peptide domains. We demonstrate that this conservation is likely due to intra-gene Concerted Evolution, which has to our knowledge not previously been reported for toxin genes. We propose that the Concerted Evolution of toxin domains provides a hitherto unrecognised way to circumvent the effects of the costly Evolutionary arms race considered to drive toxin gene Evolution by ensuring efficient secretion of ecologically important predatory toxins.
Josep A Rossello - One of the best experts on this subject based on the ideXlab platform.
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Concerted Evolution of multigene families and homoeologous recombination
2012Co-Authors: Gonzalo Nieto Feliner, Josep A RosselloAbstract:The dynamism of genomes is one of the most thoroughly documented paradigms in the genomic era, envisaged by the cytogenetic school during middle decades of the twentieth century. Such dynamism refers not just to the Evolutionary changes that take place across deep time but also to the myriad changes at different levels (from SNPs to large structural rearrangements) that shape and adjust genomes over a smaller time scale. This chapter reviews two of the many forces that provide genome dynamism in plants. These two forces, Concerted Evolution of multigene families and homoeologous recombination of hybridized genomes, in principle contribute to shape the plant genomes through opposite effects but, in fact, the both represent some of the most important manifestations of non-independent Evolution of DNA sequences.
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can extensive reticulation and Concerted Evolution result in a cladistically structured molecular data set
Cladistics, 2001Co-Authors: Gonzalo Nieto Feliner, Javier Fuertes Aguilar, Josep A RosselloAbstract:Hierarchy is the main criterion for informativeness in a data set, even if no explicit reference to Evolution as a causal process is provided. Sequence data (nuclear ribosomal DNA ITS) from Armeria (Plumbaginaceae) contains a certain amount of hierarchical structure as suggested by data decisiveness and distribution of tree lengths. However, ancillary evidence suggests that extensive gene flow and biased Concerted Evolution in these multicopy regions have significantly shaped the ITS data set. This argument is discussed using parsimony analysis of four data sets, constructed by combining wild sequences with those from different generations of artificial hybrids (wild + F1, F2, and backcrosses; wild + backcrosses; wild + F1; wild + F2). Compared to the F1 hybrids, F2 show a certain degree of homogenization in polymorphic sites. This effect reduces topological disruption caused by F1 and is considered to be illustrative of how extensive gene flow and biased Concerted Evolution may have modeled the wild ITS data. The possibility that hierarchy has arisen as a result of—or despite a significant contribution from—those two such potentially perturbing forces raises the question of what kind of signal are we recovering from this molecular data set.
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regular articlecan extensive reticulation and Concerted Evolution result in a cladistically structured molecular data set
Cladistics, 2001Co-Authors: Gonzalo Nieto Feliner, Javier Fuertes Aguilar, Josep A RosselloAbstract:Hierarchy is the main criterion for informativeness in a data set, even if no explicit reference to Evolution as a causal process is provided. Sequence data (nuclear ribosomal DNA ITS) from Armeria (Plumbaginaceae) contains a certain amount of hierarchical structure as suggested by data decisiveness and distribution of tree lengths. However, ancillary evidence suggests that extensive gene flow and biased Concerted Evolution in these multicopy regions have significantly shaped the ITS data set. This argument is discussed using parsimony analysis of four data sets, constructed by combining wild sequences with those from different generations of artificial hybrids (wild + F1, F2, and backcrosses; wild + backcrosses; wild + F1; wild + F2). Compared to the F1 hybrids, F2 show a certain degree of homogenization in polymorphic sites. This effect reduces topological disruption caused by F1 and is considered to be illustrative of how extensive gene flow and biased Concerted Evolution may have modeled the wild ITS data. The possibility that hierarchy has arisen as a result of—or despite a significant contribution from—those two such potentially perturbing forces raises the question of what kind of signal are we recovering from this molecular data set.
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nuclear ribosomal dna nrdna Concerted Evolution in natural and artificial hybrids of armeria plumbaginaceae
Molecular Ecology, 1999Co-Authors: Fuertes J Aguilar, Josep A Rossello, Nieto G FelinerAbstract:Nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences from artificial hybrids and backcrosses between Armeria villosa ssp. longiaristata and A. colorata were studied to assess the possible effects of Concerted Evolution in natural hybrids. F1 artificial hybrids show the expected pattern of additive polymorphisms for five of the six variable sites as estimated from direct sequences. However, homogenization of polymorphism is already observed in the F2, and is biased towards A. colorata except for one site. In backcrosses, an expected tendency towards homogenization of polymorphic sites in the direction of the recurrent parent is observed for five sites, although this does not necessarily imply Concerted Evolution. Conversely, the sixth site appears to elude such a mechanism and thus provides additional support for the occurrence of biased Concerted Evolution. Our findings are relevant to interpreting phylogeographic patterns involving gene flow and are also consistent with the hypothesis of a hybrid origin of A. villosa ssp. carratracensis.