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Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana.

Bush SJ, Kover PX, Urrutia AO - Mol. Ecol. (2015)

Bottom Line: We investigate the effects of exon edge conservation on the relationship of dN/dS to various sequence characteristics and gene expression parameters in the model plant Arabidopsis thaliana.Overall, we find that the effect of exon edge conservation, as well as the use of lineage-specific substitution estimates, upon dN/dS ratios partly explains the relationship between the rates of protein evolution and expression level.We conclude that lineage-specific substitutions and exon edge conservation have an important effect on dN/dS ratios and should be considered when assessing their relationship with other genomic parameters.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.

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Variables that have a significantly different correlation with dN/dS after the sequential removal of 30 codons from exon edges, compared to random codon removal. The four variables shown – expression breadth, expression level, tau and GC content – are those which have significantly different estimates of rho for their correlation with dN/dS before and after codon removal. Two criteria are met for each variable: that rho is significantly different after sequential, compared to random codon removal, and that rho is significantly different after sequential, compared to no codon removal. Estimates of dN/dS are made using alignments of A. thaliana against A.lyrata. Data for this figure, including P-values and sample sizes, are shown in Table S6 (Supporting information).
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fig02: Variables that have a significantly different correlation with dN/dS after the sequential removal of 30 codons from exon edges, compared to random codon removal. The four variables shown – expression breadth, expression level, tau and GC content – are those which have significantly different estimates of rho for their correlation with dN/dS before and after codon removal. Two criteria are met for each variable: that rho is significantly different after sequential, compared to random codon removal, and that rho is significantly different after sequential, compared to no codon removal. Estimates of dN/dS are made using alignments of A. thaliana against A.lyrata. Data for this figure, including P-values and sample sizes, are shown in Table S6 (Supporting information).

Mentions: To understand the effect of higher conservation at the exon edges on the relationships between dN/dS and other genomic parameters, we then re-analysed the correlations. We found that the correlation strength of dN/dS with several genomic features – in particular, expression level and expression breadth – decreased after the removal of exon edges. In contrast, we observed only marginal changes to these correlation coefficients after removing an equivalent number of codons from random positions (Fig.2 and Table S6 in Supporting information). This suggests that, after the removal of exon edges, the decreased correlation strength between dN/dS and genomic parameters is not explained by increased noisiness resulting from the use of shorter sequences to estimate dN/dS. It also suggests that a dN/dS-based test of selection is most acute for more highly expressed genes and that stronger correlations of dN/dS with their various characteristics reflect the stronger constraints upon them. Furthermore, when considering NI, several variables including expression level, expression breadth, the total number of introns and various measures of gene length become marginally, but significantly, stronger predictors of NI (Table S6 in Supporting information). Nevertheless, the relative order of these parameters as predictors of dN/dS remains largely unchanged with expression level still the dominant predictor.


Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana.

Bush SJ, Kover PX, Urrutia AO - Mol. Ecol. (2015)

Variables that have a significantly different correlation with dN/dS after the sequential removal of 30 codons from exon edges, compared to random codon removal. The four variables shown – expression breadth, expression level, tau and GC content – are those which have significantly different estimates of rho for their correlation with dN/dS before and after codon removal. Two criteria are met for each variable: that rho is significantly different after sequential, compared to random codon removal, and that rho is significantly different after sequential, compared to no codon removal. Estimates of dN/dS are made using alignments of A. thaliana against A.lyrata. Data for this figure, including P-values and sample sizes, are shown in Table S6 (Supporting information).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4480654&req=5

fig02: Variables that have a significantly different correlation with dN/dS after the sequential removal of 30 codons from exon edges, compared to random codon removal. The four variables shown – expression breadth, expression level, tau and GC content – are those which have significantly different estimates of rho for their correlation with dN/dS before and after codon removal. Two criteria are met for each variable: that rho is significantly different after sequential, compared to random codon removal, and that rho is significantly different after sequential, compared to no codon removal. Estimates of dN/dS are made using alignments of A. thaliana against A.lyrata. Data for this figure, including P-values and sample sizes, are shown in Table S6 (Supporting information).
Mentions: To understand the effect of higher conservation at the exon edges on the relationships between dN/dS and other genomic parameters, we then re-analysed the correlations. We found that the correlation strength of dN/dS with several genomic features – in particular, expression level and expression breadth – decreased after the removal of exon edges. In contrast, we observed only marginal changes to these correlation coefficients after removing an equivalent number of codons from random positions (Fig.2 and Table S6 in Supporting information). This suggests that, after the removal of exon edges, the decreased correlation strength between dN/dS and genomic parameters is not explained by increased noisiness resulting from the use of shorter sequences to estimate dN/dS. It also suggests that a dN/dS-based test of selection is most acute for more highly expressed genes and that stronger correlations of dN/dS with their various characteristics reflect the stronger constraints upon them. Furthermore, when considering NI, several variables including expression level, expression breadth, the total number of introns and various measures of gene length become marginally, but significantly, stronger predictors of NI (Table S6 in Supporting information). Nevertheless, the relative order of these parameters as predictors of dN/dS remains largely unchanged with expression level still the dominant predictor.

Bottom Line: We investigate the effects of exon edge conservation on the relationship of dN/dS to various sequence characteristics and gene expression parameters in the model plant Arabidopsis thaliana.Overall, we find that the effect of exon edge conservation, as well as the use of lineage-specific substitution estimates, upon dN/dS ratios partly explains the relationship between the rates of protein evolution and expression level.We conclude that lineage-specific substitutions and exon edge conservation have an important effect on dN/dS ratios and should be considered when assessing their relationship with other genomic parameters.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.

Show MeSH