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Background  In eukaryotes, long terminal repeat (LTR) retrotransposons such as  Copia, BEL  and  Gypsy  integrate their DNA copies into the host genome using a particular type of DDE transposase called integrase (INT). The  Gypsy  INT-like transposase is also conserved in the  Polinton/Maverick  self-synthesizing DNA transposons and in the 'cut and paste' DNA transposons known as  TDD-4  and  TDD-5 . Moreover, it is known that INT is similar to bacterial transposases that belong to the IS 3 , IS 481 , IS 30  and IS 630  families. It has been suggested that LTR retrotransposons evolved from a non-LTR retrotransposon fused with a DNA transposon in early eukaryotes. In this paper we analyze a diverse superfamily of eukaryotic cut and paste DNA transposons coding for INT-like transposase and discuss their evolutionary relationship to LTR retrotransposons.    Results  A new diverse eukaryotic superfamily of DNA transposons, named  Ginger  (for ' Gypsy  INteGrasE Related') DNA transposons is defined and analyzed. Analogously to the IS 3  and IS 481  bacterial transposons, the  Ginger  termini resemble those of the  Gypsy  LTR retrotransposons. Currently,  Ginger  transposons can be divided into two distinct groups named  Ginger1  and  Ginger2/Tdd . Elements from the  Ginger1  group are characterized by approximately 40 to 270 base pair (bp) terminal inverted repeats (TIRs), and are flanked by CCGG-specific or CCGT-specific target site duplication (TSD) sequences. The  Ginger1 -encoded transposases contain an approximate 400 amino acid N-terminal portion sharing high amino acid identity to the entire  Gypsy -encoded integrases, including the YPYY motif, zinc finger, DDE domain, and, importantly, the GPY/F motif, a hallmark of  Gypsy  and endogenous retrovirus (ERV) integrases.  Ginger1  transposases also contain additional C-terminal domains: ovarian tumor (OTU)-like protease domain or Ulp1 protease domain. In vertebrate genomes, at least two host genes, which were previously thought to be derived from the  Gypsy  integrases, apparently have evolved from the  Ginger1  transposase genes. We also introduce a second  Ginger  group, designated  Ginger2/Tdd , which includes the previously reported DNA transposon  TDD-4 .    Conclusions  The  Ginger  superfamily represents eukaryotic DNA transposons closely related to LTR retrotransposons.  Ginger  elements provide new insights into the evolution of transposable elements and certain transposable element (TE)-derived genes.

Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons