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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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Distribution of relative numbers of samples in which duplicated gene pairs expressed. (a) block, (b) dispersed, and (c) tandem pairs. Each cell corresponds to a range of relative number of samples. The top-right cell represents the relative number of both members in the range of (0.8, 1.0]; the bottom-right cell represents the relative number of gene 1 in the range (0.8, 1.0] and that of gene 2 in the range of (0.0, 0.2]. Cells near the centre represent the relative number of both members close to 0.5. Gray scales indicate the number of duplicated pairs within the corresponding squares. Here we also set the expression number of gene 1 less than that of gene 2 for each duplicated pair. By the definition of relative expression number, the sum of relative expression numbers of two members should greater than or equal to one.
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Figure 3: Distribution of relative numbers of samples in which duplicated gene pairs expressed. (a) block, (b) dispersed, and (c) tandem pairs. Each cell corresponds to a range of relative number of samples. The top-right cell represents the relative number of both members in the range of (0.8, 1.0]; the bottom-right cell represents the relative number of gene 1 in the range (0.8, 1.0] and that of gene 2 in the range of (0.0, 0.2]. Cells near the centre represent the relative number of both members close to 0.5. Gray scales indicate the number of duplicated pairs within the corresponding squares. Here we also set the expression number of gene 1 less than that of gene 2 for each duplicated pair. By the definition of relative expression number, the sum of relative expression numbers of two members should greater than or equal to one.

Mentions: Next, we considered the absolute number of samples in which genes were expressed as an indicator of the expression breadth [21]. For block pairs, both members tended to express in a large number of samples (Figure 2a). Although this tendency was still recognizable for dispersed pairs, some of them had both members expressed in a small number of samples (Figure 2b). On the other hand, tandem duplicates tended to express in a small number of samples (Figure 2c). The relative expression number can be used to discriminate between redundancy, complementary and asymmetric divergence [21]. Figure 3 showed the distributions of relative number of samples for block, tandem and dispersed pairs. All three groups had a high density close to the range of (0.8, 1.0], suggesting a redundant expression mode. Nevertheless, both tandem and dispersed groups had larger proportions of pairs expressed asymmetrically and complementarily than those in the block group, and this discrepancy was more manifest for tandem duplicates (Figure 3b, c).


Expression pattern divergence of duplicated genes in rice.

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

Distribution of relative numbers of samples in which duplicated gene pairs expressed. (a) block, (b) dispersed, and (c) tandem pairs. Each cell corresponds to a range of relative number of samples. The top-right cell represents the relative number of both members in the range of (0.8, 1.0]; the bottom-right cell represents the relative number of gene 1 in the range (0.8, 1.0] and that of gene 2 in the range of (0.0, 0.2]. Cells near the centre represent the relative number of both members close to 0.5. Gray scales indicate the number of duplicated pairs within the corresponding squares. Here we also set the expression number of gene 1 less than that of gene 2 for each duplicated pair. By the definition of relative expression number, the sum of relative expression numbers of two members should greater than or equal to one.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Distribution of relative numbers of samples in which duplicated gene pairs expressed. (a) block, (b) dispersed, and (c) tandem pairs. Each cell corresponds to a range of relative number of samples. The top-right cell represents the relative number of both members in the range of (0.8, 1.0]; the bottom-right cell represents the relative number of gene 1 in the range (0.8, 1.0] and that of gene 2 in the range of (0.0, 0.2]. Cells near the centre represent the relative number of both members close to 0.5. Gray scales indicate the number of duplicated pairs within the corresponding squares. Here we also set the expression number of gene 1 less than that of gene 2 for each duplicated pair. By the definition of relative expression number, the sum of relative expression numbers of two members should greater than or equal to one.
Mentions: Next, we considered the absolute number of samples in which genes were expressed as an indicator of the expression breadth [21]. For block pairs, both members tended to express in a large number of samples (Figure 2a). Although this tendency was still recognizable for dispersed pairs, some of them had both members expressed in a small number of samples (Figure 2b). On the other hand, tandem duplicates tended to express in a small number of samples (Figure 2c). The relative expression number can be used to discriminate between redundancy, complementary and asymmetric divergence [21]. Figure 3 showed the distributions of relative number of samples for block, tandem and dispersed pairs. All three groups had a high density close to the range of (0.8, 1.0], suggesting a redundant expression mode. Nevertheless, both tandem and dispersed groups had larger proportions of pairs expressed asymmetrically and complementarily than those in the block group, and this discrepancy was more manifest for tandem duplicates (Figure 3b, c).

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