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Scott William Roy - One of the best experts on this subject based on the ideXlab platform.
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Analysis of fungal genomes reveals commonalities of Intron loss/gain and functions in Intron-poor species
2020Co-Authors: Chun Shen Lim, Scott William Roy, Brooke N. Weinstein, Chris M. BrownAbstract:ABSTRACT Current evolutionary reconstructions predict that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had Intron-rich genomes. However, some extant eukaryotes have few Introns, raising the question as to why these few Introns are retained. Here we have used recently available fungal genomes to address this question. Evolutionary reconstruction of Intron presence and absence using 263 diverse fungal species support the idea that massive Intron loss has occurred in multiple clades. The Intron densities estimated in the fungal ancestral states differ from zero to 8.28 Introns per one kbp of protein-coding gene. Massive Intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts (0.01 and 0.05 Introns/kbp on average, respectively), but also in diverse smuts and allies (e.g. Ustilago maydis, Meira miltonrushii and Malassezia globosa have 0.06, 0.10 and 0.20 Introns/kbp, respectively). To investigate the roles of Introns, we searched for their special characteristics using 1302 orthologous genes from eight Intron-poor fungi. Notably, most of these Introns are found close to the translation initiation codons. Our transcriptome and translatome data analyses showed that these Introns are from genes with both higher mRNA expression and translation efficiency. Furthermore, these Introns are common in specific classes of genes (e.g. genes involved in translation and Golgi vesicle transport), and rare in others (e.g. base-excision repair genes). Our study shows that fungal Introns have a complex evolutionary history and underappreciated roles in gene expression.
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Is Genome Complexity a Consequence of Inefficient Selection? Evidence from Intron Creation in Nonrecombining Regions.
Molecular biology and evolution, 2016Co-Authors: Scott William RoyAbstract:Genomes show remarkable variation in architecture and complexity across organisms, with large differences in genome size and in numbers of genes, gene duplicates, Introns and transposable elements. These differences have important implications for transcriptome and regulatory complexity and ultimately for organismal complexity. Numbers of spliceosomal Introns show particularly striking differences, ranging across organisms from zero to hundreds of thousands of Introns per genome. The causes of these differences remain poorly understood. According to one influential perspective, differences across species reflect the differential ability of selection in different populations to eliminate allegedly deleterious Intron-containing alleles. Direct tests of this theory have been elusive. Here, I study evolution of Intron-exon structures in genomic regions of recombination suppression (RRSs), which experience drastically reduced selective efficiency due to hitchhiking and background selection. I studied Intron creation in eight independently evolved RRSs, spanning substantial diversity phylogenetically (plants, animals, fungi and brown algae) and biologically (sex chromosomes, mating type chromosomes, genomic regions flanking self-incompatibility loci, and the Drosophila "dot" chromosome). To identify newly created Introns in RRSs, I compared Intron positions in RRS genes with those in homologous genes. I found very few Intron gains: no Intron gains were observed in 7/8 studied data sets, and only three Intron gains were observed overall (on the Drosophila dot chromosome). These results suggest that efficiency of selection may not be a major cause of differences in Intron-exon structures across organisms. Instead, rates of spontaneous Intron-creating and Intron-deleting mutations may play the central role in shaping Intron-exon structures.
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Evolutionary convergence on highly-conserved 3' Intron structures in Intron-poor eukaryotes and insights into the ancestral eukaryotic genome.
PLoS genetics, 2008Co-Authors: Manuel Irimia, Scott William RoyAbstract:The presence of spliceosomal Introns in eukaryotes raises a range of questions about genomic evolution. Along with the fundamental mysteries of Introns' initial proliferation and persistence, the evolutionary forces acting on Intron sequences remain largely mysterious. Intron number varies across species from a few Introns per genome to several Introns per gene, and the elements of Intron sequences directly implicated in splicing vary from degenerate to strict consensus motifs. We report a 50-species comparative genomic study of Intron sequences across most eukaryotic groups. We find two broad and striking patterns. First, we find that some highly Intron-poor lineages have undergone evolutionary convergence to strong 3′ consensus Intron structures. This finding holds for both branch point sequence and distance between the branch point and the 3′ splice site. Interestingly, this difference appears to exist within the genomes of green alga of the genus Ostreococcus, which exhibit highly constrained Intron sequences through most of the Intron-poor genome, but not in one much more Intron-dense genomic region. Second, we find evidence that ancestral genomes contained highly variable branch point sequences, similar to more complex modern Intron-rich eukaryotic lineages. In addition, ancestral structures are likely to have included polyT tails similar to those in metazoans and plants, which we found in a variety of protist lineages. Intriguingly, Intron structure evolution appears to be quite different across lineages experiencing different types of genome reduction: whereas lineages with very few Introns tend towards highly regular Intronic sequences, lineages with very short Introns tend towards highly degenerate sequences. Together, these results attest to the complex nature of ancestral eukaryotic splicing, the qualitatively different evolutionary forces acting on Intron structures across modern lineages, and the impressive evolutionary malleability of eukaryotic gene structures.
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Intron length distributions and gene prediction
Nucleic acids research, 2007Co-Authors: Scott William Roy, David PennyAbstract:Accurate gene prediction in eukaryotes is a difficult and subtle problem. Here we point out a useful feature of expected distributions of spliceosomal Intron lengths. Since Introns are removed from transcripts prior to translation, Intron lengths are not expected to respect coding frame, thus the number of genomic Introns that are a multiple of three bases (‘3n Introns’) should be similar to the number that are a multiple of three plus one bases (or plus two bases). Skewed predicted Intron length distributions thus suggest systematic errors in Intron prediction. For instance, a genome-wide excess of 3n Introns suggests that many internal exonic sequences have been incorrectly called Introns, whereas a deficit of 3n Introns suggests that many 3n Introns that lack stop codons have been mistaken for exonic sequence. A survey of genomic annotations for 29 diverse eukaryotic species showed that skew in Intron length distributions is a common problem. We discuss several examples of skews in genome-wide Intron length distributions that indicate systematic problems with gene prediction. We suggest that evaluation of length distributions of predicted Introns is a fast and simple method for detecting a variety of possible systematic biases in gene prediction or even problems with genome assemblies, and discuss ways in which these insights could be incorporated into genome annotation protocols.
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A Very High Fraction of Unique Intron Positions in the Intron-Rich Diatom Thalassiosira pseudonana Indicates Widespread Intron Gain
Molecular biology and evolution, 2007Co-Authors: Scott William Roy, David PennyAbstract:Although spliceosomal Introns are present in all characterized eukaryotes, Intron numbers vary dramatically, from only a handful in the entire genomes of some species to nearly 10 Introns per gene on average in vertebrates. For all previously studied Intron-rich species, significant fractions of Intron positions are shared with other widely diverged eukaryotes, indicating that 1) large numbers of the Introns date to much earlier stages of eukaryotic evolution and 2) these lineages have not passed through a very Intron-poor stage since early eukaryotic evolution. By the same token, among species that have lost nearly all of their ancestral Introns, no species is known to harbor large numbers of more recently gained Introns. These observations are consistent with the notion that Intron-dense genomes have arisen only once over the course of eukaryotic evolution. Here, we report an exception to this pattern, in the Intron-rich diatom Thalassiosira pseudonana. Only 8.1% of studied T. pseudonana Intron positions are conserved with any of a variety of divergent eukaryotic species. This implies that T. pseudonana has both 1) lost nearly all of the numerous Introns present in the diatom-apicomplexan ancestor and 2) gained a large number of new Introns since that time. In addition, that so few apparently inserted T. pseudonana Introns match the positions of Introns in other species implies that insertion of multiple Introns into homologous genic sites in eukaryotic evolution is less common than previously estimated. These results suggest the possibility that Intron-rich genomes may have arisen multiple times in evolution. These results also provide evidence that multiple Intron insertion into the same site is rare, further supporting the notion that early eukaryotic ancestors were very Intron rich.
Manyuan Long - One of the best experts on this subject based on the ideXlab platform.
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Association of Intron phases with conservation at splice site sequences and evolution of spliceosomal Introns.
Molecular biology and evolution, 1999Co-Authors: Manyuan Long, M. DeutschAbstract:How exon-Intron structures of eukaryotic genes evolved under various evolutionary forces remains unknown. The phases of spliceosomal Introns (the placement of Introns with respect to reading frame) provide an opportunity to approach this question. When a large number of nuclear Introns in protein-coding genes were analyzed, it was found that most Introns were of phase 0, which keeps codons intact. We found that the phase distribution of spliceosomal Introns is strongly correlated with the sequence conservation of splice signals in exons; the relatively underrepresented phase 2 Introns are associated with the lowest conservation, the relatively overrepresented phase 0 Introns display the highest conservation, and phase 1 Introns are intermediate. Given the detrimental effect of mutations in exon sequences near splice sites as found in molecular experiments, the underrepresentation of phase 2 Introns may be the result of deleterious-mutation-driven Intron loss, suggesting a possible genetic mechanism for the evolution of Intron-exon structures.
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Intron exon structures of eukaryotic model organisms
Nucleic Acids Research, 1999Co-Authors: Michael Deutsch, Manyuan LongAbstract:To investigate the distribution of Intron-exon structures of eukaryotic genes, we have constructed a general exon database comprising all available Intron-containing genes and exon databases from 10 eukaryotic model organisms: Homo sapiens, Mus musculus, Gallus gallus, Rattus norvegicus, Arabidopsis thaliana, Zea mays, Schizosaccharomyces pombe, Aspergillus, Caenorhabditis elegans and Drosophila. We purged redundant genes to avoid the possible bias brought about by redundancy in the databases. After discarding those questionable Introns that do not contain correct splice sites, the final database contained 17 102 Introns, 21 019 exons and 2903 independent or quasi-independent genes. On average, a eukaryotic gene contains 3.7 Introns per kb protein coding region. The exon distribution peaks around 30-40 residues and most Introns are 40-125 nt long. The variable Intron-exon structures of the 10 model organisms reveal two interesting statistical phenomena, which cast light on some previous speculations. (i) Genome size seems to be correlated with total Intron length per gene. For example, invertebrate Introns are smaller than those of human genes, while yeast Introns are shorter than invertebrate Introns. However, this correlation is weak, suggesting that other factors besides genome size may also affect Intron size. (ii) Introns smaller than 50 nt are significantly less frequent than longer Introns, possibly resulting from a minimum Intron size requirement for Intron splicing.
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Intron—exon structures of eukaryotic model organisms
Nucleic acids research, 1999Co-Authors: Michael Deutsch, Manyuan LongAbstract:To investigate the distribution of Intron-exon structures of eukaryotic genes, we have constructed a general exon database comprising all available Intron-containing genes and exon databases from 10 eukaryotic model organisms: Homo sapiens, Mus musculus, Gallus gallus, Rattus norvegicus, Arabidopsis thaliana, Zea mays, Schizosaccharomyces pombe, Aspergillus, Caenorhabditis elegans and Drosophila. We purged redundant genes to avoid the possible bias brought about by redundancy in the databases. After discarding those questionable Introns that do not contain correct splice sites, the final database contained 17 102 Introns, 21 019 exons and 2903 independent or quasi-independent genes. On average, a eukaryotic gene contains 3.7 Introns per kb protein coding region. The exon distribution peaks around 30-40 residues and most Introns are 40-125 nt long. The variable Intron-exon structures of the 10 model organisms reveal two interesting statistical phenomena, which cast light on some previous speculations. (i) Genome size seems to be correlated with total Intron length per gene. For example, invertebrate Introns are smaller than those of human genes, while yeast Introns are shorter than invertebrate Introns. However, this correlation is weak, suggesting that other factors besides genome size may also affect Intron size. (ii) Introns smaller than 50 nt are significantly less frequent than longer Introns, possibly resulting from a minimum Intron size requirement for Intron splicing.
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toward a resolution of the Introns early late debate only phase zero Introns are correlated with the structure of ancient proteins
Proceedings of the National Academy of Sciences of the United States of America, 1998Co-Authors: Sandro J De Souza, Manyuan Long, Scott William Roy, Robert J Klein, Shin Lin, Walter GilbertAbstract:We present evidence that a well defined subset of Intron positions shows a non-random distribution in ancient genes. We analyze a database of ancient conserved regions drawn from GenBank 101 to retest two predictions of the theory that the first genes were constructed by exon shuffling. These predictions are that there should be an excess of symmetric exons (and sets of exons) flanked by Introns of the same phase (positions within the codon) and that Intron positions in ancient proteins should correlate with the boundaries of compact protein modules. Both these predictions are supported by the data, with considerable statistical force (P values < 0.0001). Intron positions correlate to modules of diameters around 21, 27, and 33 A, and this correlation is due to phase zero Introns. We suggest that 30-40% of present day Intron positions in ancient genes correspond to phase zero Introns originally present in the progenote, while almost all of the remaining Intron positions correspond to Introns added, or moved, appearing equally in all three Intron phases. This proposal provides a resolution for many of the arguments of the Introns-early/Introns-late debate.
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Evolution of the Intron-exon structure of eukaryotic genes
Current opinion in genetics & development, 1995Co-Authors: Manyuan Long, S. J. De Souza, Walter GilbertAbstract:The origin and evolution of Intron-exon structures continue to be controversial topics. Two alternative theories, the 'exon theory of genes' and the 'insertional theory of Introns', debate the presence or absence of Introns in primordial genes. Both sides of the argument have focused on the positions of Introns with respect to protein and gene structures. A new approach has emerged in the study of the evolution of Intron-exon structures: a population analysis of genes. One example is the statistical analysis of Intron phases--the position of Introns within or between codons. This analysis detected a significant signal of exon shuffling in the DNA sequence database containing both ancient and modern exon sequences: Intron phase correlations, that is, the association together within genes of Introns of the same phase. The results of this analysis suggest that exon shuffling played an important role in the origin of both ancient and modern genes.
Steven Zimmerly - One of the best experts on this subject based on the ideXlab platform.
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origin and evolution of the chloroplast trnk matk Intron a model for evolution of group ii Intron rna structures
Molecular Biology and Evolution, 2006Co-Authors: Georg Hausner, Robert Olson, Dawn M Simon, Ian Johnson, Erin R Sanders, Kenneth G Karol, Richard M Mccourt, Steven ZimmerlyAbstract:The trnK Intron of plants encodes the matK open reading frame (ORF), which has been used extensively as a phylogenetic marker for classification of plants. Here we examined the evolution of the trnK Intron itself as a model for group II Intron evolution in plants. Representative trnK Intron sequences were compiled from species spanning algae to angiosperms, and four Introns were newly sequenced. Phylogenetic analyses showed that the matK ORFs belong to the ML (mitochondrial-like) subclass of group II Intron ORFs, indicating that they were derived from a mobile group II Intron of the class. RNA structures of the Introns were folded and analyzed, which revealed progressive RNA structural deviations and degenerations throughout plant evolution. The data support a model in which plant organellar group II Introns were derived from bacterial-like Introns that had "standard" RNA structures and were competent for self-splicing and mobility and that subsequently the ribozyme structures degenerated to ultimately become dependent upon host-splicing factors. We propose that the patterns of RNA structure evolution seen for the trnK Intron will apply to the other group II Introns in plants.
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Mobile Group II Introns
Annual Review of Genetics, 2004Co-Authors: Alan M. Lambowitz, Steven ZimmerlyAbstract:Mobile group II Introns, found in bacterial and organellar genomes, are both catalytic RNAs and retrotransposable elements. They use an extraordinary mobility mechanism in which the excised Intron RNA reverse splices directly into a DNA target site and is then reverse transcribed by the Intron-encoded protein. After DNA insertion, the Introns remove themselves by protein-assisted, autocatalytic RNA splicing, thereby minimizing host damage. Here we discuss the experimental basis for our current understanding of group II Intron mobility mechanisms, beginning with genetic observations in yeast mitochondria, and culminating with a detailed understanding of molecular mechanisms shared by organellar and bacterial group II Introns. We also discuss recently discovered links between group II Intron mobility and DNA replication, new insights into group II Intron evolution arising from bacterial genome sequencing, and the evolutionary relationship between group II Introns and both eukaryotic spliceosomal Introns and non-LTR-retrotransposons. Finally, we describe the development of mobile group II Introns into gene-targeting vectors, "targetrons," which have programmable target specificity.
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Mobile group II Introns.
Annual Review of Genetics, 2004Co-Authors: Alan M. Lambowitz, Steven ZimmerlyAbstract:▪ Abstract Mobile group II Introns, found in bacterial and organellar genomes, are both catalytic RNAs and retrotransposable elements. They use an extraordinary mobility mechanism in which the excised Intron RNA reverse splices directly into a DNA target site and is then reverse transcribed by the Intron-encoded protein. After DNA insertion, the Introns remove themselves by protein-assisted, autocatalytic RNA splicing, thereby minimizing host damage. Here we discuss the experimental basis for our current understanding of group II Intron mobility mechanisms, beginning with genetic observations in yeast mitochondria, and culminating with a detailed understanding of molecular mechanisms shared by organellar and bacterial group II Introns. We also discuss recently discovered links between group II Intron mobility and DNA replication, new insights into group II Intron evolution arising from bacterial genome sequencing, and the evolutionary relationship between group II Introns and both eukaryotic spliceosomal ...
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Identification of a family of group II Introns encoding LAGLIDADG ORFs typical of group I Introns.
RNA (New York N.Y.), 2002Co-Authors: Navtej Toor, Steven ZimmerlyAbstract:Group I and group II Introns are unrelated classes of Introns that each encode proteins that facilitate Intron splicing and Intron mobility. Here we describe a new subfamily of nine Introns in fungi that are group II Introns but encode LAGLIDADG ORFs typical of group I Introns. The Introns have fairly standard group IIB1 RNA structures and are inserted into three different sites in SSU and LSU rRNA genes. Therefore, Introns should not be assumed to be group I Introns based solely on the presence of a LAGLIDADG ORF.
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Coevolution of group II Intron RNA structures with their Intron-encoded reverse transcriptases.
RNA (New York N.Y.), 2001Co-Authors: Navtej Toor, Georg Hausner, Steven ZimmerlyAbstract:Catalytic RNAs are often regarded as molecular fossils from the RNA World, yet it is usually difficult to get more specific information about their evolution. Here we have investigated the coevolution of group II Intron RNA structures with their Intron-encoded reverse transcriptases (RTs). Unlike group I Introns, there has been no obvious reshuffling between Intron RNA structures and ORFs. Of the six classes of Intron structures that encode ORFs, three are conventional forms of group II A1, B1, and B2 secondary structures, whereas the remaining classes are bacterial, are possibly associated with the most primitive ORFs, and have unusual features and hybrid features of group IIA and group IIB Intron structures. Based on these data, we propose a new model for the evolution of group II Introns, designated the retroelement ancestor hypothesis, which predicts that the major RNA structural forms of group II Introns developed through coevolution with the Intron-encoded protein rather than as independent catalytic RNAs, and that most ORF-less Introns are derivatives of ORF-containing Introns. The model is supported by the distribution of ORF-containing and ORF-less Introns, and by numerous examples of ORF-less Introns that contain ORF remnants.
Robert D. Hinrichsen - One of the best experts on this subject based on the ideXlab platform.
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Extremely short 20–33 nucleotide Introns are the standard length in Paramecium tetraurelia
Nucleic acids research, 1994Co-Authors: Chris B. Russell, Dean Fraga, Robert D. HinrichsenAbstract:Paramecium tetraurelia has the shortest known Introns as its standard Intron length. Sequenced Introns vary between 20 and 33 nucleotides in length. The Intron sequences were discovered in genomic sequences coding for a variety of different proteins, including phosphatases, kinases, and low-molecular weight GTP-binding proteins. All Intron sequences begin with the conserved dinucleotide GT and end with the conserved dinucleotide AG. The sequences are more AT rich than the Paramecium coding sequences. The identified sequences were confirmed as Introns by sequencing several cDNA fragments. We report here analysis of the characteristics of 50 separate Introns, including size, base composition, and a consensus sequence.
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extremely short 20 33 nucleotide Introns are the standard length in paramecium tetraurelia
Nucleic Acids Research, 1994Co-Authors: Chris B. Russell, Dean Fraga, Robert D. HinrichsenAbstract:Paramecium tetraurelia has the shortest known Introns as its standard Intron length. Sequenced Introns vary between 20 and 33 nucleotides in length. The Intron sequences were discovered in genomic sequences coding for a variety of different proteins, including phosphatases, kinases, and low-molecular weight GTP-binding proteins. All Intron sequences begin with the conserved dinucleotide GT and end with the conserved dinucleotide AG. The sequences are more AT rich than the Paramecium coding sequences. The identified sequences were confirmed as Introns by sequencing several cDNA fragments. We report here analysis of the characteristics of 50 separate Introns, including size, base composition, and a consensus sequence.
Walter Gilbert - One of the best experts on this subject based on the ideXlab platform.
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The evolution of spliceosomal Introns: patterns, puzzles and progress
Nature Reviews Genetics, 2006Co-Authors: Scott William Roy, Walter GilbertAbstract:The origins and importance of spliceosomal Introns comprise one of the longest-abiding mysteries of molecular evolution. Considerable debate remains over several aspects of the evolution of spliceosomal Introns, including the timing of Intron origin and proliferation, the mechanisms by which Introns are lost and gained, and the forces that have shaped Intron evolution. Recent important progress has been made in each of these areas. Patterns of Intron-position correspondence between widely diverged eukaryotic species have provided insights into the origins of the vast differences in Intron number between eukaryotic species, and studies of specific cases of Intron loss and gain have led to progress in understanding the underlying molecular mechanisms and the forces that control Intron evolution. Recent studies have uncovered the extent and pattern of conservation of Intron position across widely diverged eukaryotic species. Introns that are found in the genomes of modern species are mainly fairly old, with significant fractions dating to relatively deep eukaryotic ancestors. Conservation of spliceosomal components across diverse eukaryotic lineages suggests the presence of a complex spliceosome in the ancestor of all extant eukaryotes. This pattern of conservation might indicate that Introns were already numerous in early eukaryotes, with diverse eukaryotic lineages having subsequently experienced more Intron loss than gain, although debate is ongoing. Analysis of apparent cases of Intron loss indicates that such loss might occur through recombination between the genomic copy of the gene and a reverse transcript of a spliced mRNA copy of the gene. Analysis of Introns that seem to have been gained over the past 10–100 million years indicates that the new Introns could arise as transposon insertions into contiguous coding sequence, not by transposition of previous Introns, which was the previously favoured model. Previous proposals for the causes of the vast differences between numbers of Introns between eukaryotic species, which were based on inter-specific differences in either the selective value of Introns or population size, have trouble explaining the apparently large numbers of Introns in fairly deep eukaryotic ancestors. We propose that many of these Intron-number differences could be explained by Intron-loss rates. Spliceosomal Introns are thought to have had a central role in shaping modern genomes. Recent studies have shed new light on the timing of Intron evolution, mechanisms of Intron loss and gain, and the forces that have driven these processes.
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the evolution of spliceosomal Introns patterns puzzles and progress
Nature Reviews Genetics, 2006Co-Authors: Scott William Roy, Walter GilbertAbstract:The origins and importance of spliceosomal Introns comprise one of the longest-abiding mysteries of molecular evolution. Considerable debate remains over several aspects of the evolution of spliceosomal Introns, including the timing of Intron origin and proliferation, the mechanisms by which Introns are lost and gained, and the forces that have shaped Intron evolution. Recent important progress has been made in each of these areas. Patterns of Intron-position correspondence between widely diverged eukaryotic species have provided insights into the origins of the vast differences in Intron number between eukaryotic species, and studies of specific cases of Intron loss and gain have led to progress in understanding the underlying molecular mechanisms and the forces that control Intron evolution.
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The pattern of Intron loss.
Proceedings of the National Academy of Sciences of the United States of America, 2005Co-Authors: Scott William Roy, Walter GilbertAbstract:We studied Intron loss in 684 groups of orthologous genes from seven fully sequenced eukaryotic genomes. We found that Introns closer to the 3′ ends of genes are preferentially lost, as predicted if Introns are lost through gene conversion with a reverse transcriptase product of a spliced mRNA. Adjacent Introns tend to be lost in concert, as expected if such events span multiple Intron positions. Directly contrary to the expectations of some, Introns that do not interrupt codons (phase zero) are more, not less, likely to be lost, an intriguing and previously unappreciated result. Adjacent Introns with matching phases are not more likely to be retained, as would be expected if they enjoyed a relative selective advantage. The findings of 3′ and phase zero Intron loss biases are in direct contradiction to an extremely recent study of fungi Intron evolution. All patterns are less pronounced in the lineage leading to Caenorhabditis elegans, suggesting that the process of Intron loss may be qualitatively different in nematodes. Our results support a reverse transcriptase-mediated model of Intron loss.
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Mystery of Intron gain.
Genome research, 2003Co-Authors: Alexei Fedorov, Larisa Fedorova, Scott William Roy, Walter GilbertAbstract:For nearly 15 years, it has been widely believed that many Introns were recently acquired by the genes of multicellular organisms. However, the mechanism of acquisition has yet to be described for a single animal Intron. Here, we report a large-scale computational analysis of the human, Drosophila melanogaster, Caenorhabditis elegans, and Arabidopsis thaliana genomes. We divided 147,796 human Intron sequences into batches of similar lengths and aligned them with each other. Different types of homologies between Introns were found, but none showed evidence of simple Intron transposition. Also, 106,902 plant, 39,624 Drosophila, and 6021 C. elegans Introns were examined. No single case of homologous Introns in nonhomologous genes was detected. Thus, we found no example of transposition of Introns in the last 50 million years in humans, in 3 million years in Drosophila and C. elegans, or in 5 million years in Arabidopsis. Either new Introns do not arise via transposition of other Introns or Intron transposition must have occurred so early in evolution that all traces of homology have been lost.
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The signal of ancient Introns is obscured by Intron density and homolog number
Proceedings of the National Academy of Sciences of the United States of America, 2002Co-Authors: Scott William Roy, Alexei Fedorov, Walter GilbertAbstract:In ancient genes whose products have known 3-dimensional structures, an excess of phase zero Introns (those that lie between the codons) appear in the boundaries of modules, compact regions of the polypeptide chain. These excesses are highly significant and could support the hypothesis that ancient genes were assembled by exon shuffling involving compact modules. (Phase one and two Introns, and many phase zero Introns, appear to arise later.) However, as more genes, with larger numbers of homologs and Intron positions, were examined, the effects became smaller, dropping from a 40% excess to an 8% excess as the number of Intron positions increased from 570 to 3,328, even though the statistical significance remained strong. An interpretation of this behavior is that novel inserted positions appearing in homologs washed out the signal from a finite number of ancient positions. Here we show that this is likely to be the case. Analyses of Intron positions restricted to those in genes for which relatively few Intron positions from homologs are known, or to those in genes with a small number of known homologous gene structures, show a significant correlation of phase zero Intron positions with the module structure, which weakens as the density of attributed Intron positions or the number of homologs increases. These effects do not appear for phase one and phase two Introns. This finding matches the expectation of the mixed model of Intron origin, in which a fraction of phase zero Introns are left from the assembly of the first genes, while other Introns have been added in the course of evolution.
