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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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The rice eMAP. (A) Graphical representation of the rice genes expressed in the grain (red boxes, left), the leaf (green boxes, center) and the root (blue boxes, right) over the 12 rice chromosomes (vertical blocks). Thirty-two transcription factors expressed at least in one of the tissue involved in the experiment are indicated with a green star at the left side of the 12 chromosomes. (B) Number and percentage of annotated genes on the 12 rice chromosomes expressed in grain, leaf and root. For each rice chromosome (lines) are mentioned the number of annotated genes (second column), the number/percentage of spotted genes on the array (third and fourth column), the number/percentage of expressed genes in the grain (fifth and sixth column), the number/percentage of expressed genes in the leaf (seventh and eighth column), the number/percentage of expressed genes in the root (ninth and tenth column) and the number of gene expressed in at leaf one of the three tissues (eleventh column).
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Figure 1: The rice eMAP. (A) Graphical representation of the rice genes expressed in the grain (red boxes, left), the leaf (green boxes, center) and the root (blue boxes, right) over the 12 rice chromosomes (vertical blocks). Thirty-two transcription factors expressed at least in one of the tissue involved in the experiment are indicated with a green star at the left side of the 12 chromosomes. (B) Number and percentage of annotated genes on the 12 rice chromosomes expressed in grain, leaf and root. For each rice chromosome (lines) are mentioned the number of annotated genes (second column), the number/percentage of spotted genes on the array (third and fourth column), the number/percentage of expressed genes in the grain (fifth and sixth column), the number/percentage of expressed genes in the leaf (seventh and eighth column), the number/percentage of expressed genes in the root (ninth and tenth column) and the number of gene expressed in at leaf one of the three tissues (eleventh column).

Mentions: The fourth release of the rice genome annotation (http://www.tigr.org/tdb/e2k1/osa1/pseudomolecules/info.shtml) contains 55 890 genes including 13 237 that are related to TEs. The 42 653 non-TE-related genes were used to perform a genome-wide transcriptome analysis based on a rice oligo-array to produce a rice eMAP (cf. Figure 1A). The oligo-array consisted of 60 727 spots (70-nt oligonucleotides) from the Oryza sativa Genome Oligo Set Version 1.0 designed by Beijing Genomics Institute (21). When aligning the 60 727 oligonucleotides with the rice genome annotation (TIGR v4), 41 865 genes were associated with single unambiguous rice genes on the basis of at least 90% sequence identity with its associated gene over at least 60 bp, providing evidence of mis- and/or non-annotated genes in rice (26,27). Thus, the transcriptome experiments performed with this array allow us to study the expression pattern of 32 493 genes annotated by TIGR (corresponding to 41 865 spots on the array).Figure 1.


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)

The rice eMAP. (A) Graphical representation of the rice genes expressed in the grain (red boxes, left), the leaf (green boxes, center) and the root (blue boxes, right) over the 12 rice chromosomes (vertical blocks). Thirty-two transcription factors expressed at least in one of the tissue involved in the experiment are indicated with a green star at the left side of the 12 chromosomes. (B) Number and percentage of annotated genes on the 12 rice chromosomes expressed in grain, leaf and root. For each rice chromosome (lines) are mentioned the number of annotated genes (second column), the number/percentage of spotted genes on the array (third and fourth column), the number/percentage of expressed genes in the grain (fifth and sixth column), the number/percentage of expressed genes in the leaf (seventh and eighth column), the number/percentage of expressed genes in the root (ninth and tenth column) and the number of gene expressed in at leaf one of the three tissues (eleventh column).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

Figure 1: The rice eMAP. (A) Graphical representation of the rice genes expressed in the grain (red boxes, left), the leaf (green boxes, center) and the root (blue boxes, right) over the 12 rice chromosomes (vertical blocks). Thirty-two transcription factors expressed at least in one of the tissue involved in the experiment are indicated with a green star at the left side of the 12 chromosomes. (B) Number and percentage of annotated genes on the 12 rice chromosomes expressed in grain, leaf and root. For each rice chromosome (lines) are mentioned the number of annotated genes (second column), the number/percentage of spotted genes on the array (third and fourth column), the number/percentage of expressed genes in the grain (fifth and sixth column), the number/percentage of expressed genes in the leaf (seventh and eighth column), the number/percentage of expressed genes in the root (ninth and tenth column) and the number of gene expressed in at leaf one of the three tissues (eleventh column).
Mentions: The fourth release of the rice genome annotation (http://www.tigr.org/tdb/e2k1/osa1/pseudomolecules/info.shtml) contains 55 890 genes including 13 237 that are related to TEs. The 42 653 non-TE-related genes were used to perform a genome-wide transcriptome analysis based on a rice oligo-array to produce a rice eMAP (cf. Figure 1A). The oligo-array consisted of 60 727 spots (70-nt oligonucleotides) from the Oryza sativa Genome Oligo Set Version 1.0 designed by Beijing Genomics Institute (21). When aligning the 60 727 oligonucleotides with the rice genome annotation (TIGR v4), 41 865 genes were associated with single unambiguous rice genes on the basis of at least 90% sequence identity with its associated gene over at least 60 bp, providing evidence of mis- and/or non-annotated genes in rice (26,27). Thus, the transcriptome experiments performed with this array allow us to study the expression pattern of 32 493 genes annotated by TIGR (corresponding to 41 865 spots on the array).Figure 1.

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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Related in: MedlinePlus