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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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dN, dS, dN/dS and NI after exon edge removal. dN/dS (a), dN (b), dS (c) and NI (d) for a sample of 1443 genes with at least one fully alignable exon between A. thaliana and A. lyrata, after removing one codon at a time from exon edges (black), to a maximum of 30. The effects of random codon removal are shown in red. Distributions significantly differ when 30 codons are removed sequentially, but not randomly, compared to when no codons are removed. For sequential removal vs. no removal, Kruskal–Wallis P = 0.02 (dN/dS) and < 2.2 × 10−16 (NI). For random removal vs. no removal, Kruskal–Wallis P = 0.08 (dN/dS) and 0.49 (NI).
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fig01: dN, dS, dN/dS and NI after exon edge removal. dN/dS (a), dN (b), dS (c) and NI (d) for a sample of 1443 genes with at least one fully alignable exon between A. thaliana and A. lyrata, after removing one codon at a time from exon edges (black), to a maximum of 30. The effects of random codon removal are shown in red. Distributions significantly differ when 30 codons are removed sequentially, but not randomly, compared to when no codons are removed. For sequential removal vs. no removal, Kruskal–Wallis P = 0.02 (dN/dS) and < 2.2 × 10−16 (NI). For random removal vs. no removal, Kruskal–Wallis P = 0.08 (dN/dS) and 0.49 (NI).

Mentions: Using pairwise alignments of A. thaliana against either A. lyrata or T. parvula, we find that codon removal at the edges of exons results in increased dN, dS and dN/dS estimates when compared to estimates made after random codon removal from any position in the sequence (Fig.1 and Table S4 in Supporting information). This is observed irrespective of whether 10, 20 or 30 codons are removed (Table S4 in Supporting information). Estimates of NI were found to decrease after codon removal from the exon edges compared to random codon removal, also suggesting a weakening in the departure of sequence evolution from a neutral expectation (Fig.1 and Table S4 in Supporting information). These patterns are consistent with exon edges being under selective constraint, having fewer non-synonymous substitutions than sequence elsewhere in the gene. In general, exon edge removal shifts dN/dS values towards a range indicative of either stronger positive or relaxed purifying selection, with an overall increase in the proportion of genes potentially under adaptive selection (Table 3 and Table S5 in Supporting information).


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)

dN, dS, dN/dS and NI after exon edge removal. dN/dS (a), dN (b), dS (c) and NI (d) for a sample of 1443 genes with at least one fully alignable exon between A. thaliana and A. lyrata, after removing one codon at a time from exon edges (black), to a maximum of 30. The effects of random codon removal are shown in red. Distributions significantly differ when 30 codons are removed sequentially, but not randomly, compared to when no codons are removed. For sequential removal vs. no removal, Kruskal–Wallis P = 0.02 (dN/dS) and < 2.2 × 10−16 (NI). For random removal vs. no removal, Kruskal–Wallis P = 0.08 (dN/dS) and 0.49 (NI).
© Copyright Policy - open-access
Related In: Results  -  Collection

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fig01: dN, dS, dN/dS and NI after exon edge removal. dN/dS (a), dN (b), dS (c) and NI (d) for a sample of 1443 genes with at least one fully alignable exon between A. thaliana and A. lyrata, after removing one codon at a time from exon edges (black), to a maximum of 30. The effects of random codon removal are shown in red. Distributions significantly differ when 30 codons are removed sequentially, but not randomly, compared to when no codons are removed. For sequential removal vs. no removal, Kruskal–Wallis P = 0.02 (dN/dS) and < 2.2 × 10−16 (NI). For random removal vs. no removal, Kruskal–Wallis P = 0.08 (dN/dS) and 0.49 (NI).
Mentions: Using pairwise alignments of A. thaliana against either A. lyrata or T. parvula, we find that codon removal at the edges of exons results in increased dN, dS and dN/dS estimates when compared to estimates made after random codon removal from any position in the sequence (Fig.1 and Table S4 in Supporting information). This is observed irrespective of whether 10, 20 or 30 codons are removed (Table S4 in Supporting information). Estimates of NI were found to decrease after codon removal from the exon edges compared to random codon removal, also suggesting a weakening in the departure of sequence evolution from a neutral expectation (Fig.1 and Table S4 in Supporting information). These patterns are consistent with exon edges being under selective constraint, having fewer non-synonymous substitutions than sequence elsewhere in the gene. In general, exon edge removal shifts dN/dS values towards a range indicative of either stronger positive or relaxed purifying selection, with an overall increase in the proportion of genes potentially under adaptive selection (Table 3 and Table S5 in Supporting information).

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