scholarly journals Vanishing GC-Rich Isochores in Mammalian Genomes

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1837-1847 ◽  
Author(s):  
Laurent Duret ◽  
Marie Semon ◽  
Gwenaël Piganeau ◽  
Dominique Mouchiroud ◽  
Nicolas Galtier
Keyword(s):  
Gc Content ◽  
Synonymous Substitution ◽  
Equilibrium Analysis ◽  
Large Excess ◽  
Substitution Pattern ◽  
Origin And Evolution ◽  
Evolutionary Force ◽  
Mammalian Genomes ◽  
Human Polymorphism ◽  
Probability Of Fixation

AbstractTo understand the origin and evolution of isochores—the peculiar spatial distribution of GC content within mammalian genomes—we analyzed the synonymous substitution pattern in coding sequences from closely related species in different mammalian orders. In primate and cetartiodactyls, GC-rich genes are undergoing a large excess of GC → AT substitutions over AT → GC substitutions: GC-rich isochores are slowly disappearing from the genome of these two mammalian orders. In rodents, our analyses suggest both a decrease in GC content of GC-rich isochores and an increase in GC-poor isochores, but more data will be necessary to assess the significance of this pattern. These observations question the conclusions of previous works that assumed that base composition was at equilibrium. Analysis of allele frequency in human polymorphism data, however, confirmed that in the GC-rich parts of the genome, GC alleles have a higher probability of fixation than AT alleles. This fixation bias appears not strong enough to overcome the large excess of GC → AT mutations. Thus, whatever the evolutionary force (neutral or selective) at the origin of GC-rich isochores, this force is no longer effective in mammals. We propose a model based on the biased gene conversion hypothesis that accounts for the origin of GC-rich isochores in the ancestral amniote genome and for their decline in present-day mammals.

scholarly journals Runaway GC Evolution in Gerbil Genomes

2020 ◽  
Vol 37 (8) ◽  
pp. 2197-2210 ◽  
Author(s):  
Rodrigo Pracana ◽  
Adam D Hargreaves ◽  
John F Mulley ◽  
Peter W H Holland
Keyword(s):  
Rapid Evolution ◽  
Gc Content ◽  
Synonymous Substitution ◽  
Genomic Region ◽  
Recombination Rates ◽  
Substitution Pattern ◽  
Substitution Rates ◽  
Protein Coding ◽  
Murine Rodents ◽  
Genomic Regions

Abstract Recombination increases the local GC-content in genomic regions through GC-biased gene conversion (gBGC). The recent discovery of a large genomic region with extreme GC-content in the fat sand rat Psammomys obesus provides a model to study the effects of gBGC on chromosome evolution. Here, we compare the GC-content and GC-to-AT substitution patterns across protein-coding genes of four gerbil species and two murine rodents (mouse and rat). We find that the known high-GC region is present in all the gerbils, and is characterized by high substitution rates for all mutational categories (AT-to-GC, GC-to-AT, and GC-conservative) both at synonymous and nonsynonymous sites. A higher AT-to-GC than GC-to-AT rate is consistent with the high GC-content. Additionally, we find more than 300 genes outside the known region with outlying values of AT-to-GC synonymous substitution rates in gerbils. Of these, over 30% are organized into at least 17 large clusters observable at the megabase-scale. The unusual GC-skewed substitution pattern suggests the evolution of genomic regions with very high recombination rates in the gerbil lineage, which can lead to a runaway increase in GC-content. Our results imply that rapid evolution of GC-content is possible in mammals, with gerbil species providing a powerful model to study the mechanisms of gBGC.

scholarly journals The Genomic Geography and Evolution of Clusters of Tandemly Duplicated Genes in the Human and Mammal Genomes

2018 ◽  
Author(s):  
Juan F Ortiz ◽  
Antonis Rokas
Keyword(s):  
Human Chromosome ◽  
Olfactory Receptors ◽  
Gene Families ◽  
Pathogen Resistance ◽  
Duplicated Genes ◽  
Chromosome 19 ◽  
Fusion Event ◽  
Origin And Evolution ◽  
Mammalian Genomes ◽  
Human Chromosome 19

Clusters of duplicated genes (CTDGs) are nearly ubiquitous in life's genomes, and are associated with several well-known gene families, such as olfactory receptors, zinc fingers, and immunity-related genes, as well as with several highly variable traits, including olfaction, body plan architecture, and pathogen resistance. However, these observations are usually anecdotal, restricted to specific cases, and lacking evolutionary context. In this study, we use a robust statistical approach to characterize the CTDG repertoire and analyze the distribution of CTDGs across 18 mammal genomes, including human. We found that, on average, 18% of the genes in each species are parts of CTDGs. Although genes in CTDGs are enriched for several biological processes, these tend to be involved in the interactions between the organism and its environment. We further found that mammalian CTDGs are not uniformly distributed across chromosomes and that orthologs of the human chromosome 19 are among the most clustered chromosomes in nearly all mammalian genomes analyzed. We also found evidence that the human chromosome 19 was formed by a fusion event that occurred before the diversification of the rodent and primate lineages and maintained its high density of CTDGs during its subsequent evolution. Finally, using chromosome-level alignments across mammalian genomes, we show how the syntenic regions of the human chromosome 19 have been shrinking, increasing their gene density and possibly increasing the compactness of its CTDGs. These results suggest that CTDGs are a major feature of mammalian genomes and provide novel insights into the origin and evolution of regions with unusually high densities of CTDGs.

scholarly journals Origin and evolution of overlapping genes in the family Microviridae

2006 ◽  
Vol 87 (4) ◽  
pp. 1013-1017 ◽  
Author(s):  
Angelo Pavesi
Keyword(s):  
Purifying Selection ◽  
Synonymous Substitution ◽  
Ancestral State ◽  
Overlapping Genes ◽  
Novel Genes ◽  
Origin And Evolution ◽  
The Family ◽  
Genes Encoding ◽  
Phage Growth ◽  
Gene Overlap

The possibility of creating novel genes from pre-existing sequences, known as overprinting, is a widespread phenomenon in small viruses. Here, the origin and evolution of gene overlap in the bacteriophages belonging to the family Microviridae have been investigated. The distinction between ancestral and derived frames was carried out by comparing the patterns of codon usage in overlapping and non-overlapping genes. By this approach, a gradual increase in complexity of the phage genome – from an ancestral state lacking gene overlap to a derived state with a high density of genetic information – was inferred. Genes encoding less-essential proteins, yet playing a role in phage growth and diffusion, were predicted to be novel genes that originated by overprinting. Evaluation of the rates of synonymous and non-synonymous substitution yielded evidence for overlapping genes under positive selection in one frame and purifying selection in the alternative frame.

scholarly journals Comparative Analysis and Classification of Cassette Exons and Constitutive Exons

2017 ◽  
Vol 2017 ◽  
pp. 1-8 ◽  
Author(s):  
Ying Cui ◽  
Meng Cai ◽  
H. Eugene Stanley
Keyword(s):  
Genetic Diseases ◽  
Gc Content ◽  
High Accuracy ◽  
Common Type ◽  
Hereditary Diseases ◽  
Cassette Exon ◽  
Mammalian Genomes ◽  
Alternatively Spliced ◽  
Underlying Mechanisms

Alternative splicing (AS) is a major engine that drives proteome diversity in mammalian genomes and is a widespread cause of human hereditary diseases. More than 95% of genes in the human genome are alternatively spliced, and the most common type of AS is the cassette exon. Recent discoveries have demonstrated that the cassette exon plays an important role in genetic diseases. To discover the formation mechanism of cassette exon events, we statistically analyze cassette exons and find that cassette exon events are strongly influenced by individual exons that are smaller in size and that have a lower GC content, more codon terminations, and weaker splice sites. We propose an improved random-forest-based hybrid method of distinguishing cassette exons from constitutive exons. Our method achieves a high accuracy in classifying cassette exons and constitutive exons and is verified to outperform previous approaches. It is anticipated that this study will facilitate a better understanding of the underlying mechanisms in cassette exons.

Rates of Nucleotide Substitution and Mammalian Nuclear Gene Evolution: Approximate and Maximum-Likelihood Methods Lead to Different Conclusions

Genetics ◽  
2000 ◽  
Vol 156 (3) ◽  
pp. 1299-1308 ◽  
Author(s):  
Joseph P Bielawski ◽  
Katherine A Dunn ◽  
Ziheng Yang
Keyword(s):  
Maximum Likelihood ◽  
Gc Content ◽  
Synonymous Substitution ◽  
Likelihood Methods ◽  
Approximate Methods ◽  
Substitution Rates ◽  
The Third ◽  
Maximum Likelihood Methods ◽  
Codon Positions ◽  
Synonymous Substitution Rates

Abstract Rates and patterns of synonymous and nonsynonymous substitutions have important implications for the origin and maintenance of mammalian isochores and the effectiveness of selection at synonymous sites. Previous studies of mammalian nuclear genes largely employed approximate methods to estimate rates of nonsynonymous and synonymous substitutions. Because these methods did not account for major features of DNA sequence evolution such as transition/transversion rate bias and unequal codon usage, they might not have produced reliable results. To evaluate the impact of the estimation method, we analyzed a sample of 82 nuclear genes from the mammalian orders Artiodactyla, Primates, and Rodentia using both approximate and maximum-likelihood methods. Maximum-likelihood analysis indicated that synonymous substitution rates were positively correlated with GC content at the third codon positions, but independent of nonsynonymous substitution rates. Approximate methods, however, indicated that synonymous substitution rates were independent of GC content at the third codon positions, but were positively correlated with nonsynonymous rates. Failure to properly account for transition/transversion rate bias and unequal codon usage appears to have caused substantial biases in approximate estimates of substitution rates.

scholarly journals GC-Content Evolution in Mammalian Genomes: The Biased Gene Conversion Hypothesis

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 907-911 ◽  
Author(s):  
N Galtier ◽  
G Piganeau ◽  
D Mouchiroud ◽  
L Duret
Keyword(s):  
Gene Conversion ◽  
Gc Content ◽  
Biased Gene Conversion ◽  
Mammalian Genomes

scholarly journals Reconstruction of body mass evolution in the Cetartiodactyla and mammals using phylogenomic data

2017 ◽  
Author(s):  
E. Figuet ◽  
M. Ballenghien ◽  
N. Lartillot ◽  
N. Galtier
Keyword(s):  
Body Mass ◽  
Substitution Rate ◽  
Evolutionary Biology ◽  
Gc Content ◽  
Evolutionary Process ◽  
Synonymous Substitution ◽  
Molecular Data ◽  
Large Species ◽  
Data Set ◽  
Peer Community

ABSTRACTThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100042).Reconstructing ancestral characters on a phylogeny is an arduous task because the observed states at the tips of the tree correspond to a single realization of the underlying evolutionary process. Recently, it was proposed that ancestral traits can be indirectly estimated with the help of molecular data, based on the fact that life history traits influence substitution rates. Here we challenge these new approaches in the Cetartiodactyla, a clade of large mammals which, according to paleontology, derive from small ancestors. Analysing transcriptome data in 41 species, of which 22 were newly sequenced, we provide a dated phylogeny of the Cetartiodactyla and report a significant effect of body mass on the overall substitution rate, the synonymous vs. non-synonymous substitution rate and the dynamics of GC-content. Our molecular comparative analysis points toward relatively small Cetartiodactyla ancestors, in agreement with the fossil record, even though our data set almost exclusively consists of large species. This analysis demonstrates the potential of phylogenomic methods for ancestral trait reconstruction and gives credit to recent suggestions that the ancestor to placental mammals was a relatively large and long-lived animal.

scholarly journals Phylogenomics of Selaginellaceae with special reference to the enigmatic sanguinolenta group

2019 ◽  
Author(s):  
Hong-Rui Zhang ◽  
Ran Wei ◽  
Qiao-Ping Xiang ◽  
Xian-Chun Zhang
Keyword(s):  
Substitution Rate ◽  
Gc Content ◽  
Synonymous Substitution ◽  
Morphological Characters ◽  
Phylogenetic Position ◽  
Basal Clade ◽  
Phylogenetic Framework ◽  
Phylogenomic Analyses ◽  
The Stability

AbstractSelaginellaceae has been repeatedly proved as monophyly by previous studies with only one genus being recognized. However, the subgeneric classification has been debated during the recent decades. Furthermore, phylogenetic position of the newly identified sanguinolenta group has not been resolved, varying depending on the datasets and analysis methods. We carried out the phylogenomic analyses of twenty-six species from Selaginellaceae with ten species being newly sequenced and three species representing the sanguinolenta group. Four of the ten newly sequenced plastomes are assembled into the complete molecules, whereas the other six species are only assembled into five to sixteen contigs owing to high numbers of repeats. The phylogenetic framework from our study is basically congruent with the subgeneric classification of Weststrand and Korall (2016b). The position of sanguinolenta group was resolved as the basal clade in subg. Stachygynandrum, which support the position β proposed by Weststrand and Korall (2016a), also supported by the morphological characters of dimorphic vegetative leaves, monomorphic sporophylls and intermixed sporangial arrangements. Both values of dS, dN and GC content in Selaginellaceae plastomes were significantly higher than those of other lycophytes (Isoetaceae and Lycopodiaceae). The correlation analysis showed that the elevated synonymous substitution rate was significantly correlated with the high GC content in Selaginellaceae. Besides, the values of dS and dN differs significantly between branches in the phylogenetic tree of Selaginellaceae. We propose that both high GC content and the extensive RNA editing sites contributed to the elevated substitution rate in Selaginellaceae, and all of these three factors could influence the stability of phylogenetic topology of Selaginellaceae.

Local Recombination and Mutation Effects on Molecular Evolution in Drosophila

Genetics ◽  
1999 ◽  
Vol 153 (3) ◽  
pp. 1285-1296 ◽  
Author(s):  
Toshiyuki Takano-Shimizu
Keyword(s):  
Molecular Evolution ◽  
X Chromosome ◽  
Codon Bias ◽  
Synonymous Substitution ◽  
Mutational Bias ◽  
Recombination Rates ◽  
Substitution Pattern ◽  
Noncoding Regions ◽  
Significant Difference ◽  
Drosophila Yakuba

Abstract I studied the cause of the significant difference in the synonymous-substitution pattern found in the achaete-scute complex genes in two Drosophila lineages, higher codon bias in Drosophila yakuba, and lower bias in D. melanogaster. Besides these genes, the functionally unrelated yellow gene showed the same substitution pattern, suggesting a region-dependent phenomenon in the X-chromosome telomere. Because the numbers of A/T → G/C substitutions were not significantly different from those of G/C → A/T in the yellow noncoding regions of these species, a AT/GC mutational bias could not completely account for the synonymous-substitution biases. In contrast, we did find an ~14-fold difference in recombination rates in the X-chromosome telomere regions between the two species, suggesting that the reduction of recombination rates in this region resulted in the reduction of the efficacy of selection in D. melanogaster. In addition, the D. orena yellow showed a 5% increase in the G + C content at silent sites in the coding and noncoding regions since the divergence from D. erecta. This pattern was significantly different from those at the orena Adh and Amy loci. These results suggest that local changes in recombination rates and mutational pressures are contributing to the irregular synonymous-substitution patterns in Drosophila.

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