Annals of Botany 95/1 © Annals of Botany Company 2005; all rights reserved
Mechanisms of Recent Genome Size Variation in Flowering Plants
1 Department of Genetics and 2 Departments of Crop and Soil Sciences and Plant Biology, University of Georgia, Athens, GA 30602, USA
* For correspondence. E-mail maize{at}uga.edu
Received: 12 December 2003 Returned for revision: 19 January 2004 Accepted: 22 April 2004
• Background and Aims Plant nuclear genomes vary tremendously in DNA content, mostly due to differences in ancestral ploidy and variation in the degree of transposon amplification. These processes can increase genome size, but little is known about mechanisms of genome shrinkage and the degree to which these can attenuate or reverse genome expansion. This research focuses on characterizing DNA removal from the rice and Arabidopsis genomes, and discusses whether loss of DNA has effectively competed with amplification in these species.
• Methods Retrotransposons were analyzed for sequence variation within several element families in rice and Arabidopsis. Nucleotide sequence changes in the two termini of individual retrotransposons were used to date their time of insertion.
• Key Results An accumulation of small deletions was found in both species, caused by unequal homologous recombination and illegitimate recombination. The relative contribution of unequal homologous recombination compared to illegitimate recombination was higher in rice than in Arabidopsis. However, retrotransposons are rapidly removed in both species, as evidenced by the similar apparent ages of intact elements (most less than 3 million years old) in these two plants and all other investigated plant species.
• Conclusions Differences in the activity of mechanisms for retrotransposon regulation or deletion generation between species could explain current genome size variation without any requirement for natural selection to act on this trait, although the results do not preclude selection as a contributing factor. The simplest model suggests that significant genome size variation is generated by lineage-specific differences in the molecular mechanisms of DNA amplification and removal, creating major variation in nuclear DNA content that can then serve as the substrate for fitness-based selection.
Key words: Deletion, illegitimate recombination, insertion, retrotransposon, unequal recombination
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