Isolation and characterization of three interspersed repeated DNA sequences in the western whip snake (Hierophis viridiflavus)

To date the knowledge of repeated elements in the snake genome is scarce and mostly limited to various satellite and microsatellite sequences, found in species belonging to different taxonomic groups. In a wider study concerning phylogeography of the European whip snake, Hierophis viridiflavus, we identified three new repeated sequences. Then, we performed a study aimed at characterizing these sequences, underlining their principal features with particular regard to nucleotide composition, genomic quantification and chromosome localization. Two of the three repeated sequences differed in length (240 and 360 bp, respectively), but showed a 5’ segment of about 110 bp with an identity higher than 90%. Moreover this shared segment showed a trait of 85 bp with an identity of 77% with an interspersed L1element of Anolis carolinensis. Both sequences of 240 and 360 bp are organized as interspersed elements and almost exclusively localised on the W sex chromosome, representing about 0,6% of the genome. The third sequence, long about 240 bp, did not show any significant identity with the other two isolated sequences and with any other database deposited sequences. This sequence, too, is an interspersed element, representing about 2% of the genome. Differently from the other two W specific sequences, this third repeated sequence is interspersed on both autosomes and Z W sex chromosomes. We identified three new interspersed repeated sequences in H. viridiflavus. Two of them are W-specific elements related to an L1 elemnt of A. carolenesis. The third sequence is a unknown interspersed element, localised on both autosome and ZW sex chromosomes. Comparative genomic and chromosome hybridizations on other related snakes provided useful systematic and phylogentic information.