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Protein subcellular relocalization of duplicated genes in Arabidopsis.

Liu SL, Pan AQ, Adams KL - Genome Biol Evol (2014)

Bottom Line: We identified potential sequence mutations through comparative analysis that likely result in relocalization of two duplicated gene products.We show that four cases of relocalization have new expression patterns, compared with orthologs in outgroup species, including two with novel expression in pollen.This study provides insights into subcellular relocalization of evolutionarily recent gene duplicates and features of genes whose products have been relocalized.

View Article: PubMed Central - PubMed

Affiliation: Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada Present address: Department of Life Science, Tunghai University, Taichung, Taiwan.

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Asymmetric sequence evolution in duplicated gene pairs. (A) Diagram showing the frequency of asymmetrically evolved duplicated pairs in duplicated pairs with different subcellular localization (SCL) and duplicated pairs with the same SCL. (B) Histogram showing the distribution of the difference in frequency of asymmetric sequence evolution between duplicated pairs with different SCL and those with the same SCL (DIFsim) from 10,000 Monte Carlo randomization tests. Red line indicates the observed value (DIFobs).
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evu191-F2: Asymmetric sequence evolution in duplicated gene pairs. (A) Diagram showing the frequency of asymmetrically evolved duplicated pairs in duplicated pairs with different subcellular localization (SCL) and duplicated pairs with the same SCL. (B) Histogram showing the distribution of the difference in frequency of asymmetric sequence evolution between duplicated pairs with different SCL and those with the same SCL (DIFsim) from 10,000 Monte Carlo randomization tests. Red line indicates the observed value (DIFobs).

Mentions: After relocalization, a duplicated gene could perform a similar function, or there could be functional diversification compared with the ancestral function. Asymmetric sequence rate evolution, where one copy has experienced a significantly elevated rate of amino acid changes relative to the other copy, can be used as an indicator for possible functional divergence (e.g., Dermitzakis and Clark 2001; Blanc and Wolfe 2004; Kim and Yi 2006; Byrne and Wolfe 2007). To evaluate whether there has been any significant asymmetric sequence evolution for the 19 duplicate pairs with divergent localization, and to test the hypothesis that relocalized duplicates show more cases of asymmetric sequence rate evolution than those with the same subcellular localization, we identified orthologs of each duplicate from outgroup species and performed asymmetric sequence rate analysis (e.g., Blanc and Wolfe 2004; Liu et al. 2011; see Materials and Methods for details). Based on our analysis, 8 of 19 relocalized duplicates (42%) and 13 of 109 nonrelocalized duplicates (12%) showed significant asymmetric sequence evolution (table 1; LRT: Q < 0.05 in supplementary table S3, Supplementary Material online; false discovery rate-corrected for multiple tests). The protein sequences of duplicated pairs with subcellular relocalization evolve asymmetrically more frequently than those without subcellular relocalization (Fisher’s exact test: One-tailed P = 4 × 10–3; Monte Carlo randomization test: Two-tailed P = 9 × 10–4; fig. 2). We also compared the frequency of relocalized duplicate gene pairs with asymmetric sequence evolution obtained here with gene pairs from Blanc and Wolfe (2004), who analyzed 833 duplicated gene pairs from the α-WGD using the same method to what we used. A randomization test using results from Blanc and Wolfe (2004) showed that the percentage of gene pairs with asymmetric rate evolution was significantly lower than for the relocalized gene duplicates studied here (P = 0.038).Fig. 2.—


Protein subcellular relocalization of duplicated genes in Arabidopsis.

Liu SL, Pan AQ, Adams KL - Genome Biol Evol (2014)

Asymmetric sequence evolution in duplicated gene pairs. (A) Diagram showing the frequency of asymmetrically evolved duplicated pairs in duplicated pairs with different subcellular localization (SCL) and duplicated pairs with the same SCL. (B) Histogram showing the distribution of the difference in frequency of asymmetric sequence evolution between duplicated pairs with different SCL and those with the same SCL (DIFsim) from 10,000 Monte Carlo randomization tests. Red line indicates the observed value (DIFobs).
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Related In: Results  -  Collection

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evu191-F2: Asymmetric sequence evolution in duplicated gene pairs. (A) Diagram showing the frequency of asymmetrically evolved duplicated pairs in duplicated pairs with different subcellular localization (SCL) and duplicated pairs with the same SCL. (B) Histogram showing the distribution of the difference in frequency of asymmetric sequence evolution between duplicated pairs with different SCL and those with the same SCL (DIFsim) from 10,000 Monte Carlo randomization tests. Red line indicates the observed value (DIFobs).
Mentions: After relocalization, a duplicated gene could perform a similar function, or there could be functional diversification compared with the ancestral function. Asymmetric sequence rate evolution, where one copy has experienced a significantly elevated rate of amino acid changes relative to the other copy, can be used as an indicator for possible functional divergence (e.g., Dermitzakis and Clark 2001; Blanc and Wolfe 2004; Kim and Yi 2006; Byrne and Wolfe 2007). To evaluate whether there has been any significant asymmetric sequence evolution for the 19 duplicate pairs with divergent localization, and to test the hypothesis that relocalized duplicates show more cases of asymmetric sequence rate evolution than those with the same subcellular localization, we identified orthologs of each duplicate from outgroup species and performed asymmetric sequence rate analysis (e.g., Blanc and Wolfe 2004; Liu et al. 2011; see Materials and Methods for details). Based on our analysis, 8 of 19 relocalized duplicates (42%) and 13 of 109 nonrelocalized duplicates (12%) showed significant asymmetric sequence evolution (table 1; LRT: Q < 0.05 in supplementary table S3, Supplementary Material online; false discovery rate-corrected for multiple tests). The protein sequences of duplicated pairs with subcellular relocalization evolve asymmetrically more frequently than those without subcellular relocalization (Fisher’s exact test: One-tailed P = 4 × 10–3; Monte Carlo randomization test: Two-tailed P = 9 × 10–4; fig. 2). We also compared the frequency of relocalized duplicate gene pairs with asymmetric sequence evolution obtained here with gene pairs from Blanc and Wolfe (2004), who analyzed 833 duplicated gene pairs from the α-WGD using the same method to what we used. A randomization test using results from Blanc and Wolfe (2004) showed that the percentage of gene pairs with asymmetric rate evolution was significantly lower than for the relocalized gene duplicates studied here (P = 0.038).Fig. 2.—

Bottom Line: We identified potential sequence mutations through comparative analysis that likely result in relocalization of two duplicated gene products.We show that four cases of relocalization have new expression patterns, compared with orthologs in outgroup species, including two with novel expression in pollen.This study provides insights into subcellular relocalization of evolutionarily recent gene duplicates and features of genes whose products have been relocalized.

View Article: PubMed Central - PubMed

Affiliation: Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada Present address: Department of Life Science, Tunghai University, Taichung, Taiwan.

Show MeSH