Molecular and evolutionary characterization of the transposable element Uhu from Hawaiian Drosophila

Abstract

I report the complete nucleotide sequence of three independent isolates of the transposable element Uhu from Drosophila heteroneura (an endemic Hawaiian Drosophila). The complete element is about 1650 base-pairs (bp) long, has 4650 bp inverse imperfect repeats at its ends, and contains a large open reading frame potentially encoding a 251 amino acid protein. The three randomly selected isolates of Uhu which I sequenced share 93.3% nucleotide sequence identity, indicating that Uhu is well conserved within the D. heteroneura genome. I demonstrate that Uhu belongs to a class of transposable elements which includes Tc1 from Caenorhabditis elegans, Barney from Caenorhabditis briggsae, and HB1 from Drosophila melanogaster. All of these elements share significant sequence similarity, are approximately 1600 base pairs long, have short inverse terminal repeats (ITRs), contain open reading frames (ORFs) with significant sequence identity, and appear to insert specifically at TA sequences generating target site duplications. Uhu has been found in five species of endemic Hawaiian Drosophila; D. heteroneura, D. silvestris, D. differens, D. planitibia, and D. picticornis. Because the phylogenetic relationship and approximate divergence times for these species are known, I was able to examine the evolutionary dynamics of Uhu. I have sequenced a 447 bp fragment from a total of 12 Uhu elements from these species. These data provides evidence for the degeneration of Uhu in D. picticornis indicating that it is being lost in this species. The nucleotide substitution rate of Uhu is estimated to be 1.02 x 10-8substitutions/position/year which is comparable to the estimated rate for structural genes in these flies. Phylogenetic analysis using distance matrix methods confirms previously proposed phylogenetic models of these Drosophila species indicating that Uhu has been distributed among these species by vertical transmission.