Abstract
The evolutionary dynamics of Ty1-copia group retrotransposons in grass were examined by reverse transcriptase (RT) domain analysis. Twenty-three rice RT sequences were newly determined for this report. Phylogenetic analysis of 177 RT sequences, mostly derived from wheat, rice, and, maize, showed four distinct families, which were designated G1, G2, G3, and G4. Three of these families have elements obtained from distantly related species, indicative of origins prior to the radiation of grass species. Results of Southern hybridization and detailed comparisons between the wheat and rice sequences indicated that each of the families had undergone a distinct pattern of evolution. Multiple families appear to have evolved in parallel in a host species. Analyses of synonymous and nonsynonymous substitutions suggested that there is a low percentage of elements carrying functional RT domains in the G4 family, indicating that the production of new G4 elements has been controlled by a small number of elements carrying functional RT domains.
Highlights
Ty1-copia group retrotransposons are one of the best characterized groups of plant retrotransposons
The reverse transcriptase (RT) sequences of Ty1-copia group retrotransposons were amplified by PCR from rice (Oryza sativa) and were cloned and sequenced
The nucleotide sequences of these clones were successfully aligned with many other plant Ty1copia group RT sequences, evidence that they are authentic
Summary
Ty1-copia group retrotransposons are one of the best characterized groups of plant retrotransposons They have sequences called long terminal repeats (LTRs) at both ends and carry regions encoding gag, proteinase, endonuclease, reverse transcriptase (RT), and RNase H between the LTRs in the order typically observed for Ty1 of Saccharomyces and copia of Drosophila (Grandbastien 1992). The majority of plant Ty1-copia group retrotransposons, like other plant retroelements, are thought to be rarely active (see Bennetzen 1996 for review) Their expression and transposition, are inducible by such stresses as protoplast isolation and tissue culture, as well as by pathogen-related stresses (Grandbastien, Spielmann, and Caboche 1989; Hirochika 1993; Pouteau, Grandbastien, and Boccara 1994; Moreau-Mhiri et al 1996; Mhiri et al 1997). Culture-inducible activation of an element in rice called Tos has been proposed for insertional mutagenesis and gene function analysis (Hirochika et al 1996b)
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