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Structure and expression analysis of rice paleo duplications.

Throude M, Bolot S, Bosio M, Pont C, Sarda X, Quraishi UM, Bourgis F, Lessard P, Rogowsky P, Ghesquiere A, Murigneux A, Charmet G, Perez P, Salse J - Nucleic Acids Res. (2009)

Bottom Line: Improved sequence alignment criteria were used to characterize 10 major chromosome-to-chromosome duplication relationships associated with 1440 paralogous pairs, covering 47.8% of the rice genome, with 12.6% of genes that are conserved within sister blocks.Using a micro-array experiment, a genome-wide expression map has been produced, in which 2382 genes show significant differences of expression in root, leaf and grain.On the basis of a Gene Ontology analysis, we have identified and characterized the gene families that have been structurally and functionally preferentially retained in the duplication showing that the vast majority (>85%) of duplicated have been either lost or have been subfunctionalized or neofunctionalized during 50-70 million years of evolution.

View Article: PubMed Central - PubMed

Affiliation: UMR 1095 INRA/UBP, Génétique, Diversité et Ecophysiologie des Céréales (GDEC), Domaine de Crouelle, 234, 63100 Clermont Ferrand, France.

ABSTRACT
Having a well-known history of genome duplication, rice is a good model for studying structural and functional evolution of paleo duplications. Improved sequence alignment criteria were used to characterize 10 major chromosome-to-chromosome duplication relationships associated with 1440 paralogous pairs, covering 47.8% of the rice genome, with 12.6% of genes that are conserved within sister blocks. Using a micro-array experiment, a genome-wide expression map has been produced, in which 2382 genes show significant differences of expression in root, leaf and grain. By integrating both structural (1440 paralogous pairs) and functional information (2382 differentially expressed genes), we identified 115 paralogous gene pairs for which at least one copy is differentially expressed in one of the three tissues. A vast majority of the 115 paralogous gene pairs have been neofunctionalized or subfunctionalized as 88%, 89% and 96% of duplicates, respectively, expressed in grain, leaf and root show distinct expression patterns. On the basis of a Gene Ontology analysis, we have identified and characterized the gene families that have been structurally and functionally preferentially retained in the duplication showing that the vast majority (>85%) of duplicated have been either lost or have been subfunctionalized or neofunctionalized during 50-70 million years of evolution.

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Comparative expression pattern of rice paralogs. (A) Percentage of conserved expression (purple) and neofunctionalization (blue) between rice paralogs in the grain, the leaf and the root tissues. (B) Ten comparative expression profiles between rice paralogs expressed in the grain. Within 10 boxes are shown the expression profiles observed in the grain for paralogous gene pairs corresponding to the duplications between r1–r5, r2–r6, r3–r7, r7–r10 and r11–r12.
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Figure 4: Comparative expression pattern of rice paralogs. (A) Percentage of conserved expression (purple) and neofunctionalization (blue) between rice paralogs in the grain, the leaf and the root tissues. (B) Ten comparative expression profiles between rice paralogs expressed in the grain. Within 10 boxes are shown the expression profiles observed in the grain for paralogous gene pairs corresponding to the duplications between r1–r5, r2–r6, r3–r7, r7–r10 and r11–r12.

Mentions: When we compared the 1440 paralogous gene pairs to the 2382 expressed genes, we identified 115 gene pairs for which at least one gene copy was significantly expressed in one of the three tissues but only 14 gene pairs with significant expression for both copies. The remaining paralogous pairs were either not present on the array or not differentially expressed in our experiment. This result contradicts recent findings from genome-wide transcription analyses in rice using tiling arrays developed by Li et al. (26), in which the authors examined the transcriptional relationship between 1217 (compared to 1440 in the present study) marker pairs defining the same duplication events described here. They concluded that there was no significant difference in expression between the two genes forming paralagous pairs for all the duplications except some pairs of r4–r10 and r8–r9. Both the array and the probe used by the authors were fundamentally different from ours; in fact, they used a rice genome wide tiling array and, more importantly, a cDNA mixture from different tissues (shoots, roots, panicules and suspension cultures) rather than separate probes from each tissue. The mixed nature of the probe may well have masked expression differences in particular tissues, if both genes are expressed more strongly in a second tissue. In addition, the correlation was calculated on average intensity values that made it difficult to identify precise cut-off values to distinguish background noise from significant expression. In our data set, 88% of the gene pairs present were associated with a complete loss of expression for one of the paralogs in one of the three tissues involved. Figure 4A illustrates the percentage of paralogous couples for which only one copy was expressed in a given tissue (neofunctionalization) or for which both copies are expressed (conserved function). Considering a total of 84 paralogous gene pairs for the grain, 37 for the leaf and 55 for the root, for respectively 88%, 89% and 96% of them only one paralogous copy is expressed in the considered tissue, leading to the conclusion that a vast majority of paralogous pairs were neofunctionalized.Figure 4.


Structure and expression analysis of rice paleo duplications.

Throude M, Bolot S, Bosio M, Pont C, Sarda X, Quraishi UM, Bourgis F, Lessard P, Rogowsky P, Ghesquiere A, Murigneux A, Charmet G, Perez P, Salse J - Nucleic Acids Res. (2009)

Comparative expression pattern of rice paralogs. (A) Percentage of conserved expression (purple) and neofunctionalization (blue) between rice paralogs in the grain, the leaf and the root tissues. (B) Ten comparative expression profiles between rice paralogs expressed in the grain. Within 10 boxes are shown the expression profiles observed in the grain for paralogous gene pairs corresponding to the duplications between r1–r5, r2–r6, r3–r7, r7–r10 and r11–r12.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2651813&req=5

Figure 4: Comparative expression pattern of rice paralogs. (A) Percentage of conserved expression (purple) and neofunctionalization (blue) between rice paralogs in the grain, the leaf and the root tissues. (B) Ten comparative expression profiles between rice paralogs expressed in the grain. Within 10 boxes are shown the expression profiles observed in the grain for paralogous gene pairs corresponding to the duplications between r1–r5, r2–r6, r3–r7, r7–r10 and r11–r12.
Mentions: When we compared the 1440 paralogous gene pairs to the 2382 expressed genes, we identified 115 gene pairs for which at least one gene copy was significantly expressed in one of the three tissues but only 14 gene pairs with significant expression for both copies. The remaining paralogous pairs were either not present on the array or not differentially expressed in our experiment. This result contradicts recent findings from genome-wide transcription analyses in rice using tiling arrays developed by Li et al. (26), in which the authors examined the transcriptional relationship between 1217 (compared to 1440 in the present study) marker pairs defining the same duplication events described here. They concluded that there was no significant difference in expression between the two genes forming paralagous pairs for all the duplications except some pairs of r4–r10 and r8–r9. Both the array and the probe used by the authors were fundamentally different from ours; in fact, they used a rice genome wide tiling array and, more importantly, a cDNA mixture from different tissues (shoots, roots, panicules and suspension cultures) rather than separate probes from each tissue. The mixed nature of the probe may well have masked expression differences in particular tissues, if both genes are expressed more strongly in a second tissue. In addition, the correlation was calculated on average intensity values that made it difficult to identify precise cut-off values to distinguish background noise from significant expression. In our data set, 88% of the gene pairs present were associated with a complete loss of expression for one of the paralogs in one of the three tissues involved. Figure 4A illustrates the percentage of paralogous couples for which only one copy was expressed in a given tissue (neofunctionalization) or for which both copies are expressed (conserved function). Considering a total of 84 paralogous gene pairs for the grain, 37 for the leaf and 55 for the root, for respectively 88%, 89% and 96% of them only one paralogous copy is expressed in the considered tissue, leading to the conclusion that a vast majority of paralogous pairs were neofunctionalized.Figure 4.

Bottom Line: Improved sequence alignment criteria were used to characterize 10 major chromosome-to-chromosome duplication relationships associated with 1440 paralogous pairs, covering 47.8% of the rice genome, with 12.6% of genes that are conserved within sister blocks.Using a micro-array experiment, a genome-wide expression map has been produced, in which 2382 genes show significant differences of expression in root, leaf and grain.On the basis of a Gene Ontology analysis, we have identified and characterized the gene families that have been structurally and functionally preferentially retained in the duplication showing that the vast majority (>85%) of duplicated have been either lost or have been subfunctionalized or neofunctionalized during 50-70 million years of evolution.

View Article: PubMed Central - PubMed

Affiliation: UMR 1095 INRA/UBP, Génétique, Diversité et Ecophysiologie des Céréales (GDEC), Domaine de Crouelle, 234, 63100 Clermont Ferrand, France.

ABSTRACT
Having a well-known history of genome duplication, rice is a good model for studying structural and functional evolution of paleo duplications. Improved sequence alignment criteria were used to characterize 10 major chromosome-to-chromosome duplication relationships associated with 1440 paralogous pairs, covering 47.8% of the rice genome, with 12.6% of genes that are conserved within sister blocks. Using a micro-array experiment, a genome-wide expression map has been produced, in which 2382 genes show significant differences of expression in root, leaf and grain. By integrating both structural (1440 paralogous pairs) and functional information (2382 differentially expressed genes), we identified 115 paralogous gene pairs for which at least one copy is differentially expressed in one of the three tissues. A vast majority of the 115 paralogous gene pairs have been neofunctionalized or subfunctionalized as 88%, 89% and 96% of duplicates, respectively, expressed in grain, leaf and root show distinct expression patterns. On the basis of a Gene Ontology analysis, we have identified and characterized the gene families that have been structurally and functionally preferentially retained in the duplication showing that the vast majority (>85%) of duplicated have been either lost or have been subfunctionalized or neofunctionalized during 50-70 million years of evolution.

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