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Comparing the retention mechanisms of tandem duplicates and retrogenes in human and mouse genomes.

Wang Z, Dong X, Ding G, Li Y - Genet. Sel. Evol. (2010)

Bottom Line: The duplicability of tandem duplicates is also higher than that of retrogenes.However, positive selection seems to play significant roles in the retention of both types of duplicates.We propose that dosage effect is more prevalent in the retention of tandem duplicates, while 'escape from adaptive conflict' (EAC) effect is more prevalent in the retention of retrogenes.

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Affiliation: Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, PR China.

ABSTRACT

Background: Multiple models have been proposed to interpret the retention of duplicated genes. In this study, we attempted to compare whether the duplicates arising from tandem duplications and retropositions are retained by the same mechanisms in human and mouse genomes.

Results: Both sequence and expression similarity analyses revealed that tandem duplicates tend to be more conserved, whereas retrogenes tend to be more divergent. The duplicability of tandem duplicates is also higher than that of retrogenes. However, positive selection seems to play significant roles in the retention of both types of duplicates.

Conclusions: We propose that dosage effect is more prevalent in the retention of tandem duplicates, while 'escape from adaptive conflict' (EAC) effect is more prevalent in the retention of retrogenes.

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Role of positive selection. (A) Comparison of dN/dS ratios for tandem duplicates and retrogenes (log-scale). The non-synonymous substitutions in most duplicates are under selective constraints (dN/dS < 1); there is little difference in the dN/dS ratios between both types of duplicates (human: p = 0.607, mouse: p= 0.257, t-test) (B) Distribution of the duplicates before and after the split of human and mouse lineages (≈80 million years ago [33]). dS/2 was used to estimate the duplication age, which can be translated to the absolute time scale by using 2.5e-3 substitutions per site per million years [9]; there are significantly more tandem duplicates and retrogenes arising in the mouse-specific lineage (p < 1e-4 for both types, chi-square test)
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Figure 4: Role of positive selection. (A) Comparison of dN/dS ratios for tandem duplicates and retrogenes (log-scale). The non-synonymous substitutions in most duplicates are under selective constraints (dN/dS < 1); there is little difference in the dN/dS ratios between both types of duplicates (human: p = 0.607, mouse: p= 0.257, t-test) (B) Distribution of the duplicates before and after the split of human and mouse lineages (≈80 million years ago [33]). dS/2 was used to estimate the duplication age, which can be translated to the absolute time scale by using 2.5e-3 substitutions per site per million years [9]; there are significantly more tandem duplicates and retrogenes arising in the mouse-specific lineage (p < 1e-4 for both types, chi-square test)

Mentions: As mentioned in the section Background, the retention mechanisms are determined by both functional divergence and evolutionary forces. To compare the evolutionary forces for both types of duplicates, we first performed the traditional dN/dS analysis (Figure 4A). The result shows little difference in the dN/dS ratios between tandem duplicates and retrogenes (human: p = 0.607, mouse: p = 0.257, t-test). In addition, the non-synonymous substitutions in most duplicates are under selective constraints (dN/dS < 1).


Comparing the retention mechanisms of tandem duplicates and retrogenes in human and mouse genomes.

Wang Z, Dong X, Ding G, Li Y - Genet. Sel. Evol. (2010)

Role of positive selection. (A) Comparison of dN/dS ratios for tandem duplicates and retrogenes (log-scale). The non-synonymous substitutions in most duplicates are under selective constraints (dN/dS < 1); there is little difference in the dN/dS ratios between both types of duplicates (human: p = 0.607, mouse: p= 0.257, t-test) (B) Distribution of the duplicates before and after the split of human and mouse lineages (≈80 million years ago [33]). dS/2 was used to estimate the duplication age, which can be translated to the absolute time scale by using 2.5e-3 substitutions per site per million years [9]; there are significantly more tandem duplicates and retrogenes arising in the mouse-specific lineage (p < 1e-4 for both types, chi-square test)
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2902415&req=5

Figure 4: Role of positive selection. (A) Comparison of dN/dS ratios for tandem duplicates and retrogenes (log-scale). The non-synonymous substitutions in most duplicates are under selective constraints (dN/dS < 1); there is little difference in the dN/dS ratios between both types of duplicates (human: p = 0.607, mouse: p= 0.257, t-test) (B) Distribution of the duplicates before and after the split of human and mouse lineages (≈80 million years ago [33]). dS/2 was used to estimate the duplication age, which can be translated to the absolute time scale by using 2.5e-3 substitutions per site per million years [9]; there are significantly more tandem duplicates and retrogenes arising in the mouse-specific lineage (p < 1e-4 for both types, chi-square test)
Mentions: As mentioned in the section Background, the retention mechanisms are determined by both functional divergence and evolutionary forces. To compare the evolutionary forces for both types of duplicates, we first performed the traditional dN/dS analysis (Figure 4A). The result shows little difference in the dN/dS ratios between tandem duplicates and retrogenes (human: p = 0.607, mouse: p = 0.257, t-test). In addition, the non-synonymous substitutions in most duplicates are under selective constraints (dN/dS < 1).

Bottom Line: The duplicability of tandem duplicates is also higher than that of retrogenes.However, positive selection seems to play significant roles in the retention of both types of duplicates.We propose that dosage effect is more prevalent in the retention of tandem duplicates, while 'escape from adaptive conflict' (EAC) effect is more prevalent in the retention of retrogenes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, PR China.

ABSTRACT

Background: Multiple models have been proposed to interpret the retention of duplicated genes. In this study, we attempted to compare whether the duplicates arising from tandem duplications and retropositions are retained by the same mechanisms in human and mouse genomes.

Results: Both sequence and expression similarity analyses revealed that tandem duplicates tend to be more conserved, whereas retrogenes tend to be more divergent. The duplicability of tandem duplicates is also higher than that of retrogenes. However, positive selection seems to play significant roles in the retention of both types of duplicates.

Conclusions: We propose that dosage effect is more prevalent in the retention of tandem duplicates, while 'escape from adaptive conflict' (EAC) effect is more prevalent in the retention of retrogenes.

Show MeSH