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Expression pattern divergence of duplicated genes in rice.

Li Z, Zhang H, Ge S, Gu X, Gao G, Luo J - BMC Bioinformatics (2009)

Bottom Line: We found a significant difference in expression divergence patterns for the three types of duplicated gene pairs.Consistent with previous studies on Arabidopsis, our results revealed a significant difference in expression divergence between the types of duplicated genes and a significant correlation between expression divergence and synonymous substitution rate.We found that the attribution of duplication mode to the expression divergence implies a different evolutionary course of duplicated genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center for Bioinformatics, Peking University, Beijing 100871, PR China. liz@mail.cbi.pku.edu.cn

ABSTRACT

Background: Genome-wide duplication is ubiquitous during diversification of the angiosperms, and gene duplication is one of the most important mechanisms for evolutionary novelties. As an indicator of functional evolution, the divergence of expression patterns following duplication events has drawn great attention in recent years. Using large-scale whole-genome microarray data, we systematically analyzed expression divergence patterns of rice genes from block, tandem and dispersed duplications.

Results: We found a significant difference in expression divergence patterns for the three types of duplicated gene pairs. Expression correlation is significantly higher for gene pairs from block and tandem duplications than those from dispersed duplications. Furthermore, a significant correlation was observed between the expression divergence and the synonymous substitution rate which is an approximate proxy of divergence time. Thus, both duplication types and divergence time influence the difference in expression divergence. Using a linear model, we investigated the influence of these two variables and found that the difference in expression divergence between block and dispersed duplicates is attributed largely to their different divergence time. In addition, the difference in expression divergence between tandem and the other two types of duplicates is attributed to both divergence time and duplication type.

Conclusion: Consistent with previous studies on Arabidopsis, our results revealed a significant difference in expression divergence between the types of duplicated genes and a significant correlation between expression divergence and synonymous substitution rate. We found that the attribution of duplication mode to the expression divergence implies a different evolutionary course of duplicated genes.

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Histogram of synonymous substitution rate (KS). Block pairs are indicated by blue, tandem pairs by red, and dispersed pairs by green.
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Figure 5: Histogram of synonymous substitution rate (KS). Block pairs are indicated by blue, tandem pairs by red, and dispersed pairs by green.

Mentions: Distribution of KS (Figure 5) showed that dispersed pairs had significantly higher KS values than block and tandem pairs (Mann-Whitney U test, both p values < 2.2 × 10-16), and a significant difference existed between KS of block and tandem pairs (Mann-Whitney U test, p value = 1.3 × 10-6). On the other hand, a negative correlation was observed between expression correlation and synonymous substitution rate as reported above. We further evaluated the attribution of duplication mode and KS. The conventional ANOVA was not applicable to our case since the number of gene pairs in each duplication type was extremely unbalanced. Instead, a simple linear model (formula (1)) was applied. The significance of regression coefficient can be used to indicate the attribution of the corresponding term to the difference of expression correlation. Parametric statistical test (t-test) of ordinary least square estimates (Supplementary table 1 in Additional file 1) showed that regression coefficients except for β2 and β4 were significant (p values < 0.001). Bootstrapping MM-estimates of coefficients (Supplementary table 2 in Additional file 1) also showed the same results, all coefficients but β2 and β4 were significant at 5% level. These results suggested that the difference in expression correlation between block and dispersed pairs could be mainly attributed to the difference of divergence time. On the other hand, the difference in expression correlation between tandem pairs and the other two types was attributed to the difference in both divergence time and duplication mode.


Expression pattern divergence of duplicated genes in rice.

Li Z, Zhang H, Ge S, Gu X, Gao G, Luo J - BMC Bioinformatics (2009)

Histogram of synonymous substitution rate (KS). Block pairs are indicated by blue, tandem pairs by red, and dispersed pairs by green.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2697655&req=5

Figure 5: Histogram of synonymous substitution rate (KS). Block pairs are indicated by blue, tandem pairs by red, and dispersed pairs by green.
Mentions: Distribution of KS (Figure 5) showed that dispersed pairs had significantly higher KS values than block and tandem pairs (Mann-Whitney U test, both p values < 2.2 × 10-16), and a significant difference existed between KS of block and tandem pairs (Mann-Whitney U test, p value = 1.3 × 10-6). On the other hand, a negative correlation was observed between expression correlation and synonymous substitution rate as reported above. We further evaluated the attribution of duplication mode and KS. The conventional ANOVA was not applicable to our case since the number of gene pairs in each duplication type was extremely unbalanced. Instead, a simple linear model (formula (1)) was applied. The significance of regression coefficient can be used to indicate the attribution of the corresponding term to the difference of expression correlation. Parametric statistical test (t-test) of ordinary least square estimates (Supplementary table 1 in Additional file 1) showed that regression coefficients except for β2 and β4 were significant (p values < 0.001). Bootstrapping MM-estimates of coefficients (Supplementary table 2 in Additional file 1) also showed the same results, all coefficients but β2 and β4 were significant at 5% level. These results suggested that the difference in expression correlation between block and dispersed pairs could be mainly attributed to the difference of divergence time. On the other hand, the difference in expression correlation between tandem pairs and the other two types was attributed to the difference in both divergence time and duplication mode.

Bottom Line: We found a significant difference in expression divergence patterns for the three types of duplicated gene pairs.Consistent with previous studies on Arabidopsis, our results revealed a significant difference in expression divergence between the types of duplicated genes and a significant correlation between expression divergence and synonymous substitution rate.We found that the attribution of duplication mode to the expression divergence implies a different evolutionary course of duplicated genes.

View Article: PubMed Central - HTML - PubMed

Affiliation: College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center for Bioinformatics, Peking University, Beijing 100871, PR China. liz@mail.cbi.pku.edu.cn

ABSTRACT

Background: Genome-wide duplication is ubiquitous during diversification of the angiosperms, and gene duplication is one of the most important mechanisms for evolutionary novelties. As an indicator of functional evolution, the divergence of expression patterns following duplication events has drawn great attention in recent years. Using large-scale whole-genome microarray data, we systematically analyzed expression divergence patterns of rice genes from block, tandem and dispersed duplications.

Results: We found a significant difference in expression divergence patterns for the three types of duplicated gene pairs. Expression correlation is significantly higher for gene pairs from block and tandem duplications than those from dispersed duplications. Furthermore, a significant correlation was observed between the expression divergence and the synonymous substitution rate which is an approximate proxy of divergence time. Thus, both duplication types and divergence time influence the difference in expression divergence. Using a linear model, we investigated the influence of these two variables and found that the difference in expression divergence between block and dispersed duplicates is attributed largely to their different divergence time. In addition, the difference in expression divergence between tandem and the other two types of duplicates is attributed to both divergence time and duplication type.

Conclusion: Consistent with previous studies on Arabidopsis, our results revealed a significant difference in expression divergence between the types of duplicated genes and a significant correlation between expression divergence and synonymous substitution rate. We found that the attribution of duplication mode to the expression divergence implies a different evolutionary course of duplicated genes.

Show MeSH