Given this number of potential Zorro3 insertion sites it is interesting that in our sample of 30 new insertions we identified three pairs of elements that had independently inserted at the same sites.
Because there is exceedingly small likelihood that retroposons would be precisely excised or independently inserted into exactly the same orthologous site in different lineages, a retroposon insertion is a unique, powerful, nearly homoplasy-free phylogenetic molecular marker (Shedlock and Okada 2000).
The resulting 1761-bp and 4536-bp fragments, corresponding to the ScTPO1 and ScPDR5 genes, respectively, were independently inserted via the XhoI/SpeI restriction sites into the pBA002 plasmid.
Genome walking confirmed that the Hyg and Gus T-DNA cassettes were independently inserted in different regions of the tobacco genome.
To generate Tpo1p and Pdr5p protein fusions with YFP and GFP, each coding sequence, excluding the stop codon, was PCR-amplified (Supplementary Table S1) using yeast genomic DNA as a template and independently inserted under the control of the 35S promoter via the XhoI/PacI restriction sites into the YFP- or GFP-tagged versions of the pBA002 plasmid.
For example, in [7], multiple watermarks were independently inserted into the frequency and phase of an audio signal, and in [8], the robust and semifragile watermarks were respectively embedded into the approximation and residual components of an image, while in [9], the subsampling technique was applied to an host image for the insertion of both the invisible and visible watermarks.
A total of 231 introgression lines were created from a set of 28 D. mauritiana lines bearing one copy of P[ w+] independently inserted in the 3rd chromosome.
Phylogenetic relationships based on the comparison of 5S coding sequences suggest that the 5S genes independently inserted IGS at least three times in the course of gymnosperm evolution.
More interestingly, at the same region of the CC subgenomes, we identified identical type, independently inserted Pack-MuLEs with completely different captured genomic sequences, which indicates that these genome regions may contain preferentially inserted sequence sites for this MuLE.
Thus, SPRAG1L-SPRAG2L and LVRAG1L-LVRAG2L appear to derive from two related but distinct transposons that most likely independently inserted into the purple and green sea urchin genomes a few million years ago.
