scholarly journals Unequal synonymous substitution rates within and between two protein- coding mitochondrial genes

1996 ◽  
Vol 13 (6) ◽  
pp. 889-892 ◽  
Author(s):  
J. P. Bielawski ◽  
J. R. Gold
Keyword(s):  
Synonymous Substitution ◽  
Mitochondrial Genes ◽  
Substitution Rates ◽  
Protein Coding ◽  
Synonymous Substitution Rates

scholarly journals Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants

2007 ◽  
Vol 7 (1) ◽  
pp. 135 ◽  
Author(s):  
Jeffrey P Mower ◽  
Pascal Touzet ◽  
Julie S Gummow ◽  
Lynda F Delph ◽  
Jeffrey D Palmer
Keyword(s):  
Synonymous Substitution ◽  
Mitochondrial Genes ◽  
Seed Plants ◽  
Substitution Rates ◽  
Extensive Variation ◽  
Synonymous Substitution Rates

scholarly journals Complete Chloroplast Genome Sequences of Clematis: IR Expansion and Relative Rates of Synonymous Substitutions

2018 ◽  
Author(s):  
Kyoung Su Choi ◽  
Keum Seon Jeong ◽  
Young-Ho Ha ◽  
Kyung Choi
Keyword(s):  
Chloroplast Genome ◽  
Tandem Repeats ◽  
Single Copy ◽  
Synonymous Substitution ◽  
Substitution Rates ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Repeat Structure ◽  
Chloroplast Genomes ◽  
Synonymous Substitution Rates

Genus Clematis is one of the largest within Ranunculaceae. Here we report the chloroplast genome of two Clematis species, C. brachyura and C. trichotoma endemic to Korea. The chloroplast genome lengths of C. brachyura and C. trichotoma are 159,532 bp and 159,170 bp, respectively. Gene contents in the complete chloroplast genomes of these two Clematis species are identical to that of most Ranunculaceae and other angiosperms. However, our data results demonstrated that genus Clematis has inversion and rearrangement events concerning gene rps4 gene, rps16 to trnH region, and trnL to ndhC region, and IR regions expansion. Comparison of IR regions among Ranunculaceae species revealed that Clematis species contained six protein coding genes (infA, rps8, rpl14, rpl16, rps3, and rpl22) usually found in the long single copy (LSC) region of other species. Phylogenetic analysis demonstrated that genus Clematis is closely related to genus Ranunculus. Differences in repeat structure, substitution rates, and IR expansion in genera Clematis and Ranunculus, explained their relationship. Clematis species showed slightly higher tandem repeats content than Ranunculus species. The six protein-coding genes showed lower synonymous substitution rates in the IR of Clematis species than in the LSC of Ranunculus species. Overall, the chloroplast genomes and results presented here provide important information on the evolution of Ranunculaceae.

scholarly journals Comparing Patterns of Nucleotide Substitution Rates Among Chloroplast Loci Using the Relative Ratio Test

Genetics ◽  
1997 ◽  
Vol 146 (1) ◽  
pp. 393-399 ◽  
Author(s):  
Spencer V Muse ◽  
Brandon S Gaut
Keyword(s):  
Nucleotide Substitution ◽  
Nonsynonymous Substitution ◽  
Synonymous Substitution ◽  
Joint Analysis ◽  
Ratio Test ◽  
Substitution Rates ◽  
Chloroplast Genomes ◽  
Synonymous Substitution Rates ◽  
Nucleotide Substitution Rates ◽  
Evolutionary Lineages

Even when several genetic loci are used in molecular evolutionary studies, each locus is typically analyzed independently of the others. This type of approach makes it difficult to study mechanisms and processes that affect multiple genes. In this work we develop a statistical approach for the joint analysis of two or more loci. The tests we propose examine whether or not nucleotide substitution rates across evolutionary lineages have the same relative proportions at two loci. Theses procedures are applied to 33 genes from the chloroplast genomes of rice, tobacco, pine, and liverwort. With the exception of five clearly distinct loci, we find that synonymous substitution rates tend to change proportionally across genes. We interpret these results to be consistent with a “lineage effect” acting on the entire chloroplast genome. In contrast, nonsynonymous rates do not change proportionally across genes, suggesting that locus-specific evolutionary effects dominate patterns of nonsynonymous substitution.

scholarly journals The Causes of Synonymous Rate Variation in the Rodent Genome: Can Substitution Rates Be Used to Estimate the Sex Bias in Mutation Rate?

Genetics ◽  
1999 ◽  
Vol 152 (2) ◽  
pp. 661-673 ◽  
Author(s):  
Nick G C Smith ◽  
Laurence D Hurst
Keyword(s):  
Mutation Rate ◽  
Rate Ratio ◽  
Synonymous Substitution ◽  
Sex Bias ◽  
Imprinted Genes ◽  
Rate Variation ◽  
Substitution Rates ◽  
Synonymous Substitution Rates ◽  
Male To Female ◽  
Different Parts

Abstract Miyata et al. have suggested that the male-to-female mutation rate ratio (α) can be estimated by comparing the neutral substitution rates of X-linked (X), Y-linked (Y), and autosomal (A) genes. Rodent silent site X/A comparisons provide very different estimates from X/Y comparisons. We examine three explanations for this discrepancy: (1) statistical biases and artifacts, (2) nonneutral evolution, and (3) differences in mutation rate per germline replication. By estimating errors and using a variety of methodologies, we tentatively reject explanation 1. Our analyses of patterns of codon usage, synonymous rates, and nonsynonymous rates suggest that silent sites in rodents are evolving neutrally, and we can therefore reject explanation 2. We find both base composition and methylation differences between the different sets of chromosomes, a result consistent with explanation 3, but these differences do not appear to explain the observed discrepancies in estimates of α. Our finding of significantly low synonymous substitution rates in genomically imprinted genes suggests a link between hemizygous expression and an adaptive reduction in the mutation rate, which is consistent with explanation 3. Therefore our results provide circumstantial evidence in favor of the hypothesis that the discrepancies in estimates of α are due to differences in the mutation rate per germline replication between different parts of the genome. This explanation violates a critical assumption of the method of Miyata et al., and hence we suggest that estimates of α, obtained using this method, need to be treated with caution.

scholarly journals Evolutionary Rate Heterogeneity and Functional Divergence of Orthologous Genes in Pyrus

Biomolecules ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 490 ◽  
Author(s):  
Yunpeng Cao ◽  
Lan Jiang ◽  
Lihu Wang ◽  
Yongping Cai
Keyword(s):  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Synonymous Substitution ◽  
Evolutionary Rates ◽  
Orthologous Genes ◽  
Protein Coding ◽  
Different Types ◽  
Synonymous Substitution Rates ◽  
Gene Structures

Negatively selected genes (NSGs) and positively selected genes (PSGs) are the two types of most nuclear protein-coding genes in organisms. However, the evolutionary rates and characteristics of different types of genes have been rarely understood. In the present study, we investigate the rates of synonymous substitution (Ks) and the rates of non-synonymous substitution (Ka) by comparing the orthologous genes of two sequenced Pyrus species, Pyrus bretschneideri and Pyrus communis. Subsequently, we compared the evolutionary rates, gene structures, and expression profiles during different fruit development between PSGs and NSGs. Compared with the NSGs, the PSGs have fewer exons, shorter gene length, lower synonymous substitution rates and have higher evolutionary rates. Remarkably, gene expression patterns between two Pyrus species fruit indicated functional divergence for most of the orthologous genes derived from a common ancestor, and subfunctionalization for some of them. Overall, the present study shows that PSGs differs from NSGs not only under environmental selective pressure (Ka/Ks), but also in their structural, functional, and evolutionary properties. Additionally, our resulting data provides important insights for the evolution and highlights the diversification of orthologous genes in two Pyrus species.

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.

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