title: Gene conversion in the rice genome.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing Genomics Institute, Beijing Proteomics Institute, Beijing 101300, China. shuqing.xu@env.ethz.ch
authors.forename: Shuqing
authors.initials: S
authors.lastname: Xu
authors.forename: Terry
authors.initials: T
authors.lastname: Clark
authors.forename: Hongkun
authors.initials: H
authors.lastname: Zheng
authors.forename: Søren
authors.initials: S
authors.lastname: Vang
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Xiaoguang
authors.initials: X
authors.lastname: Zheng
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D032461:Chromosomes, Plant / Q000235:genetics; D019143:Evolution, Molecular; D005785:Gene Conversion; D020440:Gene Duplication; D018745:Genome, Plant; D023281:Genomics; D008957:Models, Genetic; D005810:Multigene Family; D012275:Oryza / Q000235:genetics*; D011544:Pseudogenes; D012641:Selection, Genetic; D013045:Species Specificity