scholarly journals Rates of synonymous substitution and base composition of nuclear genes in Drosophila.

Genetics ◽  
1992 ◽  
Vol 130 (4) ◽  
pp. 855-864
Author(s):  
E N Moriyama ◽  
T Gojobori
Keyword(s):  
Nuclear Genome ◽  
Nuclear Gene ◽  
Synonymous Substitution ◽  
Selective Constraint ◽  
Nuclear Genes ◽  
Functional Genes ◽  
Silent Substitution ◽  
Codon Positions ◽  
Synonymous Substitution Rates ◽  
Mutation Pattern

Abstract We compared the rates of synonymous (silent) substitution among various genes in a number of species of Drosophila. First, we found that even for a particular gene, the rate of synonymous substitution varied considerably with Drosophila lineages. Second, we showed a large variation in synonymous substitution rates among nuclear genes in Drosophila. These rates of synonymous substitution were correlated negatively with C content and positively with A content at the third codon positions. Nucleotide sequences were also compared between pseudogenes and their functional homologs. The C content of the pseudogenes was lower than that of the functional genes and the A content of the former was higher than that of the latter. Because the synonymous substitution for functional genes and the nucleotide substitution for pseudogenes are exempted from any selective constraint at the protein level, these observations could be explained by a biased pattern of mutation in the Drosophila nuclear genome. Such a bias in the mutation pattern may affect the molecular clock (local clock) of each nuclear gene of each species. Finally, we obtained the average rates of synonymous substitution for three gene groups in Drosophila; 11.0 x 10(-9), 17.5 x 10(-9) and 27.1 x 10(-9)/site/year.

scholarly journals Banana contains a diverse array of endogenous badnaviruses

2005 ◽  
Vol 86 (2) ◽  
pp. 511-520 ◽  
Author(s):  
Andrew D. W. Geering ◽  
Neil E. Olszewski ◽  
Glyn Harper ◽  
Benham E. L. Lockhart ◽  
Roger Hull ◽  
...  
Keyword(s):  
Nuclear Genome ◽  
Synonymous Substitution ◽  
Selective Constraint ◽  
Musa Balbisiana ◽  
Reading Frame ◽  
B Genome ◽  
Species Analysis ◽  
Breeding Programmes ◽  
Distinct Sequence ◽  
High Degree

Banana streak disease is caused by several distinct badnavirus species, one of which is Banana streak Obino l'Ewai virus. Banana streak Obino l'Ewai virus has severely hindered international banana (Musa spp.) breeding programmes, as new hybrids are frequently infected with this virus, curtailing any further exploitation. This infection is thought to arise from viral DNA integrated in the nuclear genome of Musa balbisiana (B genome), one of the wild species contributing to many of the banana cultivars currently grown. In order to determine whether the DNA of other badnavirus species is integrated in the Musa genome, PCR-amplified DNA fragments from Musa acuminata, M. balbisiana and Musa schizocarpa, as well as cultivars ‘Obino l'Ewai’ and ‘Klue Tiparot’, were cloned. In total, 103 clones were sequenced and all had similarity to open reading frame III in the badnavirus genome, although there was remarkable variation, with 36 distinct sequences being recognized with less than 85 % nucleotide identity to each other. There was no commonality in the sequences amplified from M. acuminata and M. balbisiana, suggesting that integration occurred following the separation of these species. Analysis of rates of non-synonymous and synonymous substitution suggested that the integrated sequences evolved under a high degree of selective constraint as might be expected for a living badnavirus, and that each distinct sequence resulted from an independent integration event.

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 A comparison of one-rate and two-rate inference frameworks for site-specific dN/dS estimation

2015 ◽  
Author(s):  
Stephanie J. Spielman ◽  
Suyang Wan ◽  
Claus O. Wilke
Keyword(s):  
Model Misspecification ◽  
Purifying Selection ◽  
Synonymous Substitution ◽  
Selective Constraint ◽  
Model Specification ◽  
Inference Model ◽  
Specific Context ◽  
Point Estimates ◽  
Synonymous Substitution Rates ◽  
Excessive Noise

AbstractTwo broad paradigms exist for inferring dN/dS, the ratio of nonsynonymous to synonymous substitution rates, from coding sequences: i) a one-rate approach, where dN/dS is represented with a single parameter, or ii) a two-rate approach, where dN and dS are estimated separately. The performances of these two approaches have been well-studied in the specific context of proper model specification, i.e. when the inference model matches the simulation model. By contrast, the relative performances of one-rate vs. two-rate parameterizations when applied to data generated according to a different mechanism remains unclear. Here, we compare the relative merits of one-rate and two-rate approaches in the specific context of model misspecification by simulating alignments with mutation-selection models rather than with dN/dS-based models. We find that one-rate frameworks generally infer more accurate dN/dS point estimates, even when dS varies among sites. In other words, modeling dS variation may substantially reduce accuracy of dN/dS point estimates. These results appear to depend on the selective constraint operating at a given site. In particular, for sites under strong purifying selection (dN/dS<~0.3), one-rate and two-rate models show comparable performances. However, one-rate models significantly outperform two-rate models for sites under moderate-to-weak purifying selection. We attribute this distinction to the fact that, for these more quickly evolving sites, a given substitution is more likely to be nonsynonymous than synonymous. The data will therefore be relatively enriched for nonsynonymous changes, and modeling dS contributes excessive noise to dN/dS estimates. We additionally find that high levels of divergence among sequences, rather than the number of sequences in the alignment, are more critical for obtaining precise point estimates.

scholarly journals Comparative Genomic Analyses Reveal a Specific Mutation Pattern Between Human Coronavirus SARS-CoV-2 and Bat-CoV RaTG13

2020 ◽  
Vol 11 ◽  
Author(s):  
Longxian Lv ◽  
Gaolei Li ◽  
Jinhui Chen ◽  
Xinle Liang ◽  
Yudong Li
Keyword(s):  
Relative Proportion ◽  
Synonymous Substitution ◽  
Comparative Genomic ◽  
Nucleotide Substitutions ◽  
Spike Gene ◽  
Synonymous Mutations ◽  
Global Pandemic ◽  
Genomic Analyses ◽  
Synonymous Substitution Rates ◽  
Mutation Pattern

BackgroundThe outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan, China, rapidly grew into a global pandemic. How SARS-CoV-2 evolved remains unclear.MethodsWe performed a comprehensive analysis using the available genomes of SARS-CoV-2 and its closely related coronaviruses.ResultsThe ratio of nucleotide substitutions to amino acid substitutions of the spike gene (9.07) between SARS-CoV-2 WIV04 and Bat-CoV RaTG13 was markedly higher than that between other coronaviruses (range, 1.29–4.81); the ratio of non-synonymous to synonymous substitution rates (dN/dS) between SARS-CoV-2 WIV04 and Bat-CoV RaTG13 was the lowest among all the performed comparisons, suggesting evolution under stringent selective pressure. Notably, the relative proportion of the T:C transition was markedly higher between SARS-CoV-2 WIV04 and Bat-CoV RaTG13 than between other compared coronaviruses. Codon usage is similar across these coronaviruses and is unlikely to explain the increased number of synonymous mutations. Moreover, some sites of the spike protein might be subjected to positive selection.ConclusionsOur results showed an increased proportion of synonymous substitutions and the T:C transition between SARS-CoV-2 and RaTG13. Further investigation of the mutation pattern mechanism would contribute to understanding viral pathogenicity and its adaptation to hosts.

scholarly journals RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of holo-mycoheterotrophic plants

2017 ◽  
Author(s):  
M.I. Schelkunov ◽  
A.A. Penin ◽  
M.D. Logacheva
Keyword(s):  
Protein Import ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Nuclear Genes ◽  
Rna Seq ◽  
Nucleotide Substitutions ◽  
Plastid Genomes ◽  
Genome Wide ◽  
Genes Encoding ◽  
Mycoheterotrophic Plants

Summary• While photosynthesis is the most notable trait of plants, several lineages of plants (so-called holo-heterotrophs) have adapted to obtain organic compounds from other sources. The switch to heterotrophy leads to profound changes at the morphological, physiological and genomic levels.• Here, we characterize the transcriptomes of three species representing two lineages of mycoheterotrophic plants: orchids (Epipogium aphyllum and Epipogium roseum) and Ericaceae (Hypopitys monotropa). Comparative analysis is used to highlight the parallelism between distantly related holo-heterotrophic plants.• In both lineages, we observed genome-wide elimination of nuclear genes that encode proteins related to photosynthesis, while systems associated with protein import to plastids as well as plastid transcription and translation remain active. Genes encoding components of plastid ribosomes that have been lost from the plastid genomes have not been transferred to the nuclear genomes; instead, some of the encoded proteins have been substituted by homologs. The nuclear genes of both Epipogium species accumulated mutations twice as rapidly as their photosynthetic relatives; in contrast, no increase in the substitution rate was observed in H.monotropa.• Holo-heterotrophy leads to profound changes in nuclear gene content. The observed increase in the rate of nucleotide substitutions is lineage specific, rather than a universal phenomenon among non-photosynthetic plants.

scholarly journals Codon usage bias and base composition of nuclear genes in Drosophila.

Genetics ◽  
1993 ◽  
Vol 134 (3) ◽  
pp. 847-858 ◽  
Author(s):  
E N Moriyama ◽  
D L Hartl
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Nuclear Genome ◽  
Selective Constraint ◽  
Drosophila Virilis ◽  
Nuclear Genes ◽  
Selective Constraints ◽  
Synonymous Sites ◽  
The Difference ◽  
Translational Level

Abstract The nuclear genes of Drosophila evolve at various rates. This variation seems to correlate with codon-usage bias. In order to elucidate the determining factors of the various evolutionary rates and codon-usage bias in the Drosophila nuclear genome, we compared patterns of codon-usage bias with base compositions of exons and introns. Our results clearly show the existence of selective constraints at the translational level for synonymous (silent) sites and, on the other hand, the neutrality or near neutrality of long stretches of nucleotide sequence within noncoding regions. These features were found for comparisons among nuclear genes in a particular species (Drosophila melanogaster, Drosophila pseudoobscura and Drosophila virilis) as well as in a particular gene (alcohol dehydrogenase) among different species in the genus Drosophila. The patterns of evolution of synonymous sites in Drosophila are more similar to those in the prokaryotes than they are to those in mammals. If a difference in the level of expression of each gene is a main reason for the difference in the degree of selective constraint, the evolution of synonymous sites of Drosophila genes would be sensitive to the level of expression among genes and would change as the level of expression becomes altered in different species. Our analysis verifies these predictions and also identifies additional selective constraints at the translational level in Drosophila.

scholarly journals Risk of cardiac manifestations in adult mitochondrial disease caused by nuclear genetic defects

Open Heart ◽  
2021 ◽  
Vol 8 (1) ◽  
pp. e001510
Author(s):  
Albert Zishen Lim ◽  
Daniel M Jones ◽  
Matthew G D Bates ◽  
Andrew M Schaefer ◽  
John O'Sullivan ◽  
...  
Keyword(s):  
Mitochondrial Disease ◽  
Nuclear Dna ◽  
Laboratory Data ◽  
Nuclear Genome ◽  
Nuclear Gene ◽  
Left Ventricular ◽  
Adult Patients ◽  
Limited Information ◽  
Cardiac Abnormalities ◽  
Cardiac Manifestations

ObjectiveRegular cardiac surveillance is advocated for patients with primary mitochondrial DNA disease. However, there is limited information to guide clinical practice in mitochondrial conditions caused by nuclear DNA defects. We sought to determine the frequency and spectrum of cardiac abnormalities identified in adult mitochondrial disease originated from the nuclear genome.MethodsAdult patients with a genetically confirmed mitochondrial disease were identified and followed up at the national clinical service for mitochondrial disease in Newcastle upon Tyne, UK (January 2009 to December 2018). Case notes, molecular genetics reports, laboratory data and cardiac investigations, including serial electrocardiograms and echocardiograms, were reviewed.ResultsIn this cohort-based observational study, we included 146 adult patients (92 women) (mean age 53.6±18.7 years, 95% CI 50.6 to 56.7) with a mean follow-up duration of 7.9±5.1 years (95% CI 7.0 to 8.8). Eleven different nuclear genotypes were identified: TWNK, POLG, RRM2B, OPA1, GFER, YARS2, TYMP, ETFDH, SDHA, TRIT1 and AGK. Cardiac abnormalities were detected in 14 patients (9.6%). Seven of these patients (4.8%) had early-onset cardiac manifestations: hypertrophic cardiomyopathy required cardiac transplantation (AGK; n=2/2), left ventricular (LV) hypertrophy and bifascicular heart block (GFER; n=2/3) and mild LV dysfunction (GFER; n=1/3, YARS2; n=1/2, TWNK; n=1/41). The remaining seven patients had acquired heart disease most likely related to conventional cardiovascular risk factors and presented later in life (14.6±12.8 vs 55.1±8.9 years, p<0.0001).ConclusionsOur findings demonstrate that the risk of cardiac involvement is genotype specific, suggesting that routine cardiac screening is not indicated for most adult patients with nuclear gene-related mitochondrial disease.

Pseudogenized Amelogenin Reveals Early Tooth Loss in True Toads (Anura: Bufonidae)

2021 ◽  
Author(s):  
John Shaheen ◽  
Austin B Mudd ◽  
Thomas G H Diekwisch ◽  
John Abramyan
Keyword(s):  
Tooth Loss ◽  
Tooth Enamel ◽  
Synonymous Substitution ◽  
Bufo Bufo ◽  
Molecular Dating ◽  
Bufo Gargarizans ◽  
The Family ◽  
Synonymous Substitution Rates ◽  
Mandibular Teeth ◽  
Early Tooth Loss

Abstract Extant anurans (frogs and toads) exhibit reduced dentition, ranging from a lack of mandibular teeth to complete edentulation, as observed in the true toads of the family Bufonidae. The evolutionary timeline of these reductions remains vague due to a poor fossil record. Previous studies have demonstrated an association between the lack of teeth in edentulous vertebrates and the pseudogenization of the major tooth enamel gene amelogenin (AMEL) through accumulation of deleterious mutations and the disruption of its coding sequence. In the present study we have harnessed the pseudogenization of AMEL as a molecular dating tool to correlate loss of dentition with genomic mutation patterns during the rise of the family Bufonidae. Specifically, we have utilized AMEL pseudogenes in three members of the family as a tool to estimate the putative date of edentulation in true toads. Comparison of AMEL sequences from Rhinella marina, Bufo gargarizans and Bufo bufo, with nine extant, dentulous frogs, revealed mutations confirming AMEL inactivation in Bufonidae. AMEL pseudogenes in modern bufonids also exhibited remarkably high 86–93% sequence identity among each other, with only a slight increase in substitution rate and relaxation of selective pressure, in comparison to functional copies in other anurans. Moreover, using selection intensity estimates and synonymous substitution rates, analysis of functional and pseudogenized AMEL resulted in an estimated inactivation window of 46-60 MYA in the lineage leading to modern true toads, a timeline that coincides with the rise of the family Bufonidae.

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