Molecular paleontology of transposable elements from Arabidopsis thaliana

We report results of a comprehensive computer-assisted analysis of new tran sposable elements (TEs) from Arabidopsis thaliana. Our analysis revealed se veral previously unknown pogo- and En/Spm-like families and two novel super families of DNA transposons, Arnold and Harbinger. One of the En/Spm-like f amilies (Atenspm) was found to be involved in generating satellite arrays i n paracentromeric regions. Of the two superfamilies reported, Harbinger is distantly related to bacterial IS5-like insertion elements, and Arnold cont ains DNA transposons without terminal inverted repeats (TIRs), which were n ever reported in eukaryotes before. Furthermore, we report a large number o f young and diverse copia-like autonomous and nonautonomous retroelements a nd discuss their potential evolutionary relationship with mammalian retrovi ruses. The A.thaliana genome harbors copia-like retroelements which encode a putative env-like protein reported previously in the SIRE-1 retrotranspos on from soybean. Finally, we demonstrate a nonrandom chromosomal distributi on of the most abundant A.thaliana TEs clustered in the first half of chrom osome II, which includes the centromeric region. The families of TEs from A .thaliana are relatively young, extremely diverse and much smaller than tho se from mammalian genomes. We discuss the potential factors determining sim ilarities and differences in the evolution of TEs in mammals and A. thalian a.