Abstract
Much of the eukaryotic genome is known to be mobile, largely due to the movement of transposons and other parasitic elements. Recent work in plants and Drosophila suggests that mobility is also a feature of many nontransposon genes and gene families. Indeed, analysis of the Arabidopsis genome suggested that as many as half of all genes had moved to unlinked positions since Arabidopsis diverged from papaya roughly 72 million years ago, and that these mobile genes tend to fall into distinct gene families. However, the mechanism by which single gene transposition occurred was not deduced. By comparing two closely related species, Arabidopsis thaliana and Arabidopsis lyrata, we sought to determine the nature of gene transposition in Arabidopsis. We found that certain categories of genes are much more likely to have transposed than others, and that many of these transposed genes are flanked by direct repeat sequence that was homologous to sequence within the orthologous target site in A. lyrata and which was predominantly genic in identity. We suggest that intrachromosomal recombination between tandemly duplicated sequences, and subsequent insertion of the circular product, is the predominant mechanism of gene transposition.
Highlights
Much of the eukaryotic genome is known to be mobile
In order to distinguish between a gain in A. thaliana and a loss in A. lyrata, each region was compared to the orthologous regions in Carica papaya and Vitis vinefera, two more distantly related species in the rosid clade (Figure 1) (Methods)
The absence of a given gene at the syntenous position in both of the outgroups and in A. lyrata was interpreted as evidence for insertion in A. thaliana; if it was not possible to substantiate the status of the candidate in the outgroup—for example because its expected position in the outgroup was in an unsequenced region—that particular candidate was excluded
Summary
Much of the eukaryotic genome is known to be mobile This is a characteristic feature of transposable elements, and a large proportion of many eukaryotic genomes are composed of these parasitic elements. Recent work in plants [1,2] and Drosophila [3] demonstrates that mobility is a feature of many non-transposon genes and gene families. In order to detect such evidence, we examined more recent gene transposition events by comparing two relatively closely related (,5MYA, [8]) Arabidopsis species, A. thaliana and A. lyrata. In this way we were able to identify a large number of recently transposed A. thaliana genes. We found that flanking direct repeats were associated with nearly half of these transposed genes, indicating that these repeats have a role in the process of gene transposition
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