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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.

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
Gene duplicability. Distribution of the duplicates among small (≤5 members) and large (>5 members) families; tandem duplicates are more likely to be enriched in large families than the retrogenes (p < 0.01 for both genomes, chi-square test)
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Figure 1: Gene duplicability. Distribution of the duplicates among small (≤5 members) and large (>5 members) families; tandem duplicates are more likely to be enriched in large families than the retrogenes (p < 0.01 for both genomes, chi-square test)

Mentions: We identified 1,210 tandem duplicates and 410 retrogenes in the human genome, and 1,802 tandem duplicates and 680 retrogenes in the mouse genome. The higher number of tandem duplicates than retrogenes in both genomes implies a higher gene duplicability for tandem duplicates. Previous studies have found that gene duplicability is positively correlated with gene dosage [20] and gene complexity [21], although the correlation with functional essentiality is not always the same in yeasts and mammals [22-25]. To investigate the difference in gene duplicability between tandem duplicates and retrogenes in more detail, we counted the number of each type of duplicates in gene families with various sizes (Figure 1). The result shows that their distributions among gene families are quite different (p < 0.01 for both genomes, chi-square test). Specifically, tandem duplicates are more likely to be enriched in larger families, whereas retrogenes do not display a preference.


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)

Gene duplicability. Distribution of the duplicates among small (≤5 members) and large (>5 members) families; tandem duplicates are more likely to be enriched in large families than the retrogenes (p < 0.01 for both genomes, chi-square test)
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Gene duplicability. Distribution of the duplicates among small (≤5 members) and large (>5 members) families; tandem duplicates are more likely to be enriched in large families than the retrogenes (p < 0.01 for both genomes, chi-square test)
Mentions: We identified 1,210 tandem duplicates and 410 retrogenes in the human genome, and 1,802 tandem duplicates and 680 retrogenes in the mouse genome. The higher number of tandem duplicates than retrogenes in both genomes implies a higher gene duplicability for tandem duplicates. Previous studies have found that gene duplicability is positively correlated with gene dosage [20] and gene complexity [21], although the correlation with functional essentiality is not always the same in yeasts and mammals [22-25]. To investigate the difference in gene duplicability between tandem duplicates and retrogenes in more detail, we counted the number of each type of duplicates in gene families with various sizes (Figure 1). The result shows that their distributions among gene families are quite different (p < 0.01 for both genomes, chi-square test). Specifically, tandem duplicates are more likely to be enriched in larger families, whereas retrogenes do not display a preference.

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