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

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