This chapter also discusses the more recent use of transposable-element-based genetic transformation procedures in nondrosophilid insects and concludes that many of the tools required for genetic manipulations of nondrosophilid insects are now available.
In addition, despite the fact that retrogenes use machinery of transposable elements, they do not follow the transposable elements genome location pattern recently described in detail [ 20]: high density in the X chromosome and consistent bias insertion close to female and male germline expressed genes.
This method of using inactive fragments of transposable elements has been used previously to investigate patterns of background point substitution and insertion/deletions in Drosophila and other organisms [ 15, 30, 34].
It is believed that retrogenes use the machinery of transposable elements for their insertion.
Here, we use divergence estimates of transposable elements that have been active after the split of the rodent and primate lineage to assess the degree of conservation in both local mutation rate and substitutional asymmetries between human and mouse orthologs.
We examined the potential that transcripts may include transposable elements by performing a blastn (e−10) analysis using a database of transposable elements developed from randomly sampled Ipomoea purpurea genome sequence and the program Assisted Automated Assembler of Repeat Families (i.e., AAARF; Debarry et al. 2008; R. S. Baucom and J. Bennetzen, unpublished data).
Mutant induction in such annual plants by T-DNA insertior or using the mobility of transposable elements (e.g. the maize Ac element or its inactive derivate Ds) in most cases was achieved using knock-out tagging, disrupting a functional pathway by element insertion in functional genes and subsequent selfing of mutagenized plants.
A third approach employed in maize makes use of the RescueMu transposable element [ 16], relying on the fact that Mutator elements preferentially insert into low-copy-number DNA [ 17].
Although a more detailed classification system is now being used, two major classes of transposable elements (TE's) exist: retrotransposons, which transpose by using a RNA intermediate, and DNA transposons, which transpose by cutting their genomic sequence and inserting it elsewhere in the genome.
We demonstrated that orthologous transposable elements have evolved at the same rate in both lineages, therefore, we propose that the use of a large sample of transposable elements constitutes a good alternative to the use of genes to date the radiation between lineages.
