Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization

  1. Xiyin Wang1,2,
  2. Haibao Tang1,3,
  3. John E. Bowers1 and
  4. Andrew H. Paterson1,3,4
  1. 1 Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA;
  2. 2 College of Sciences, Hebei Polytechnic University, Tangshan, Hebei 063000, China;
  3. 3 Department of Plant Biology, University of Georgia, Athens, Georgia 30602, USA

    Abstract

    Whole-genome duplication produces massive duplicated blocks in plant genomes. Sharing appreciable sequence similarity, duplicated blocks may have been affected by illegitimate recombination. However, large-scale evaluation of illegitimate recombination in plant genomes has not been possible previously. Here, based on comparative and phylogenetic analysis of the sequenced genomes of rice and sorghum, we report evidence of extensive and long-lasting recombination between duplicated blocks. We estimated that at least 5.5% and 4.1% of rice and sorghum duplicated genes have been affected by nonreciprocal recombination (gene conversion) over nearly their full length after rice–sorghum divergence, while even more (8.7% and 8.1%, respectively) have been converted over portions of their length. We found that conversion occurs in higher frequency toward the terminal regions of chromosomes, and expression patterns of converted genes are more positively correlated than nonconverted ones. Though converted paralogs are more similar to one another than nonconverted ones, elevated nucleotide differences between rice–sorghum orthologs indicates that they have evolved at a faster rate, implying that recombination acts as an accelerating, rather than a conservative, element. The converted genes show no change in selection pressure. We also found no evidence that conversion contributed to guanine-cytosine (GC) content elevation.

    Footnotes

    • 4 Corresponding author.

      E-mail paterson{at}uga.edu; fax (706) 583-0160.

    • [Supplemental material is available online at www.genome.org.]

    • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.087288.108.

      • Received September 28, 2008.
      • Accepted February 24, 2009.
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