Gene conversion in the rice genome

Xu, Shuqing, Clark, Terry, Zheng, Hongkun, Vang, Søren, Li, Ruiqiang, Wong, Gane Ka-Shu, Wang, Jun and Zheng, Xiaoguang (2008) Gene conversion in the rice genome. BMC Genomics, 9 93-1-93-8. doi:10.1186/1471-2164-9-93


Author Xu, Shuqing
Clark, Terry
Zheng, Hongkun
Vang, Søren
Li, Ruiqiang
Wong, Gane Ka-Shu
Wang, Jun
Zheng, Xiaoguang
Title Gene conversion in the rice genome
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2008-02-25
Sub-type Article (original research)
DOI 10.1186/1471-2164-9-93
Open Access Status DOI
Volume 9
Start page 93-1
End page 93-8
Total pages 8
Place of publication London, England
Publisher BioMed Central
Language eng
Subject 07 Agricultural and Veterinary Sciences
0703 Crop and Pasture Production
Formatted 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 conversion 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.
Keyword Gene conversion
Q-Index Code C1
Q-Index Status Provisional Code
Additional Notes Article no. 93

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Agriculture and Food Sciences
 
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Created: Wed, 23 Dec 2009, 10:15:59 EST by Christine Ouslinis on behalf of Faculty Of Nat Resources, Agric & Veterinary Sc