Mechanisms of recent genome size variation in flowering plants

Abstract

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.

Fig. 1.

Spectrum of deletion sizes in LTR-retrotransposons of Arabidopsis and rice. Dark bars indicate Arabidopsis deletions and light bars indicate rice deletions. Deletions of specific size were pooled for this figure in ranges of 50 bp, except the first pool which records deletions of 10–50 bp. Subsequent pooled deletions sizes were 51–100 bp, 101–150 bp, 151–200 bp, etc. The data show that the respective mean and median deletion sizes were 304 bp and 50 bp for Arabidopsis, with 318 bp and 41 bp for rice.