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Gene conversion in the rice genome.

Xu S, Clark T, Zheng H, Vang S, Li R, Wong GK, Wang J, Zheng X - BMC Genomics (2008)

Bottom Line: We found that the inter-chromosomal conversions distributed between chromosome 1 and 5, 2 and 6, and 3 and 5 are more frequent than genome average (Z-test, P < 0.05).The frequencies of gene conversion on the same chromosome decreased with the physical distance between gene conversion partners.The number of conversions associated with segmentation is less than ten percent.

View Article: PubMed Central - HTML - PubMed

Affiliation: Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China. shuqing.xu@env.ethz.ch

ABSTRACT

Background: Gene conversion causes a non-reciprocal transfer of genetic information between similar sequences. Gene conversion can both homogenize genes and recruit point mutations thereby shaping the evolution of multigene families. In the rice genome, the large number of duplicated genes increases opportunities for gene conversion.

Results: To characterize gene conversion in rice, we have defined 626 multigene families in which 377 gene conversions were detected using the GENECONV program. Over 60% of the conversions we detected were between chromosomes. We found that the inter-chromosomal conversions distributed between chromosome 1 and 5, 2 and 6, and 3 and 5 are more frequent than genome average (Z-test, P < 0.05). The frequencies of gene conversion on the same chromosome decreased with the physical distance between gene conversion partners. Ka/Ks analysis indicates that gene conversion is not tightly linked to natural selection in the rice genome. To assess the contribution of segmental duplication on gene conversion statistics, we determined locations of conversion partners with respect to inter-chromosomal segment duplication. The number of conversions associated with segmentation is less than ten percent. Pseudogenes in the rice genome with low similarity to Arabidopsis genes showed greater likelihood for gene conversion than those with high similarity to Arabidopsis genes. Functional annotations suggest that at least 14 multigene families related to disease or bacteria resistance were involved in conversion events.

Conclusion: The evolution of gene families in the rice genome may have been accelerated by conversion with pseudogenes. Our analysis suggests a possible role for gene conversion in the evolution of pathogen-response genes.

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Gene conversions are favored between similar genes. Sequence similarities were calculated for homologs involved in gene conversions and for all homologs.
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Figure 3: Gene conversions are favored between similar genes. Sequence similarities were calculated for homologs involved in gene conversions and for all homologs.

Mentions: To compare the sequence similarity of gene pairs involved in conversions to gene pairs not involved in conversions, we aligned entire gene sequences as described in Methods. The fraction of gene pairs involved in conversion events had significantly higher sequence similarity compared to all gene pairs (Figure 3). To test if the converted regions themselves influenced the higher similarity in the conversion group, we also calculated similarities of genes in conversion pairs, omitting the converted regions from the analysis. No significant difference was found between before and after omitting the converted regions (data not shown); the higher sequence similarity of gene pairs involved in conversion was not only a feature of the converted regions. In fact, most gene pairs not involved in conversions share statistically significant similarities in about 30–60% of their sequences with an average sequence similarity of 45%. In contrast, gene pairs involved in conversions exhibit a greater sequence similarity in the range of 60–80%. These results are consistent with findings that gene conversion is favored between similar genes [18].


Gene conversion in the rice genome.

Xu S, Clark T, Zheng H, Vang S, Li R, Wong GK, Wang J, Zheng X - BMC Genomics (2008)

Gene conversions are favored between similar genes. Sequence similarities were calculated for homologs involved in gene conversions and for all homologs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2277409&req=5

Figure 3: Gene conversions are favored between similar genes. Sequence similarities were calculated for homologs involved in gene conversions and for all homologs.
Mentions: To compare the sequence similarity of gene pairs involved in conversions to gene pairs not involved in conversions, we aligned entire gene sequences as described in Methods. The fraction of gene pairs involved in conversion events had significantly higher sequence similarity compared to all gene pairs (Figure 3). To test if the converted regions themselves influenced the higher similarity in the conversion group, we also calculated similarities of genes in conversion pairs, omitting the converted regions from the analysis. No significant difference was found between before and after omitting the converted regions (data not shown); the higher sequence similarity of gene pairs involved in conversion was not only a feature of the converted regions. In fact, most gene pairs not involved in conversions share statistically significant similarities in about 30–60% of their sequences with an average sequence similarity of 45%. In contrast, gene pairs involved in conversions exhibit a greater sequence similarity in the range of 60–80%. These results are consistent with findings that gene conversion is favored between similar genes [18].

Bottom Line: We found that the inter-chromosomal conversions distributed between chromosome 1 and 5, 2 and 6, and 3 and 5 are more frequent than genome average (Z-test, P < 0.05).The frequencies of gene conversion on the same chromosome decreased with the physical distance between gene conversion partners.The number of conversions associated with segmentation is less than ten percent.

View Article: PubMed Central - HTML - PubMed

Affiliation: Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China. shuqing.xu@env.ethz.ch

ABSTRACT

Background: Gene conversion causes a non-reciprocal transfer of genetic information between similar sequences. Gene conversion can both homogenize genes and recruit point mutations thereby shaping the evolution of multigene families. In the rice genome, the large number of duplicated genes increases opportunities for gene conversion.

Results: To characterize gene conversion in rice, we have defined 626 multigene families in which 377 gene conversions were detected using the GENECONV program. Over 60% of the conversions we detected were between chromosomes. We found that the inter-chromosomal conversions distributed between chromosome 1 and 5, 2 and 6, and 3 and 5 are more frequent than genome average (Z-test, P < 0.05). The frequencies of gene conversion on the same chromosome decreased with the physical distance between gene conversion partners. Ka/Ks analysis indicates that gene conversion is not tightly linked to natural selection in the rice genome. To assess the contribution of segmental duplication on gene conversion statistics, we determined locations of conversion partners with respect to inter-chromosomal segment duplication. The number of conversions associated with segmentation is less than ten percent. Pseudogenes in the rice genome with low similarity to Arabidopsis genes showed greater likelihood for gene conversion than those with high similarity to Arabidopsis genes. Functional annotations suggest that at least 14 multigene families related to disease or bacteria resistance were involved in conversion events.

Conclusion: The evolution of gene families in the rice genome may have been accelerated by conversion with pseudogenes. Our analysis suggests a possible role for gene conversion in the evolution of pathogen-response genes.

Show MeSH