SINE Insertions as Clade Markers for Wild Crucifer Species

Short interspersed nuclear elements (SINEs) are small noncoding transposable elements that are widespread in most eukaryotic genomes. Plant S1 SINEs are present in crucifers, especially in species of the Brassiceae tribe, and were generated by several waves of amplification of different evolutionary ages, suggesting that S1 insertional variability (presence/absence of an S1 at a given genomic site) could be used as a classification criterion to evaluate phylogenetic relationships. We applied this strategy on closely related species from the Brassica oleracea species complex using 21 independent S1 genomic sites. The microsatellite-like variation of S1 39 poly(A) tails was also used as a complementary classification criterion to obtain internal resolution in two different clades. The phylogenetic tree obtained by this approach is in general agreement with the classification made from chloroplast DNA restriction site polymorphisms and differs significantly from two other (nonequivalent) classifications made using nuclear restriction fragment length polymorphisms. Brassica incana, Brassica montana, and Brassica hilarionis are confirmed as the closest relatives of B. oleracea. From our data, we suggest that Brassica drepanensis emerged recently from a B. incana/Brassica villosa hybrid (with B. villosa as the maternal parent) following backcrosses to B. incana. We also detected several introgressions, confirming that these highly related species are capable of genetic exchange in their natural habitat. S1 markers are therefore very useful in understanding the detailed evolutionary history of wild Brassica species and could also be used to identify potential gene flow between cultivated (including transgenic) Brassica and their wild relatives.