Supplementary Material for: Characterization and Genomic Organization of <i>PERI</i>, a Repetitive DNA in the <i>Drosophila buzzatii</i> Cluster Related to <i>DINE-1</i> Transposable Elements and Highly Abundant in the Sex Chromosomes

2010-10-08T00:00:00Z (GMT) by Kuhn G.C.S. Heslop-Harrison J.S.
<i>Background/Aims: </i>Transposable elements (TEs) are dynamic components of eukaryotic genomes. We aimed to characterize TEs to help elucidate their impact on the genomic architecture, diversity and evolution of chromosomes in the <i>D. buzzatii</i> cluster of species (<i>repleta</i> group). <i>Methods: </i>A full TE element of <i>D. buzzatii</i>, named <i>PERI</i>, was identified in a BAC clone available in GenBank. <i>PERI</i> was further analysed using bioinformatics tools, PCR and in-situ hybridization to metaphase chromosomes and DNA fibers. <i>Results: </i><i>PERI</i> shares several structures in common with <i>DINE-1</i>, an abundant TE found widespread along the <i>Drosophila</i> genus. The central region of <i>PERI</i> is very dynamic but revealed a disrupted pattern of nucleotide variability among its internal tandem repeats. The minimal sequence variation in <i>D. serido</i> suggests recent amplification. <i>PERI</i> accumulates near or at heterochromatic regions of all 6 pairs of chromosomes, especially on the sex chromosomes, with some clustering. <i>Conclusions: </i><i>PERI</i> is an abundant type of <i>DINE-1</i> transposon but with characteristic sequence signatures and probably restricted to the <i>buzzatii </i>complex. The conservation of different central domains and association with genes suggests selective constraints. Although at or near heterochromatin, the distribution of <i>PERI</i> does not overlap with satDNAs, probably a consequence of functional or molecular constraints.