Similarity of the Cin1 repetitive family of Zea mays to eukaryotic transposable elements

Abstract

It has been suggested that the middle repetitive class of sequences that make up a large proportion of the eukaryotic genome have been amplified and dispersed by DNA transposition. Transposition is a phenomenon first postulated by Barbara McClintock on the basis of her genetic analysis of mutants in Zea mays. Since then, DNA transposition has been studied genetically in various plant systems and is well documented on the molecular level in both prokaryotes and eukaryotes. This has included the isolation of DNA inserts at various loci in several plants; however, the prevalence of transposition in plants is not established. We report here DNA nucleotide sequence data which show that some members of the Cin1 middle repetitive family of maize have features characteristic of known transposable elements. One cloned Cin1 repeat has a 6-base pair (bp) perfect inverted repeat sequence at its ends. The terminal five base pairs (5' TGTTG . . . CAACA 3') are identical to the termini of Drosophila copia transposable elements. Two other Cin1 alleles are flanked by 5-bp direct repeats. A comparison is made with the long terminal repeat (LTR) of the copia-Ty1-retrovirus families of moveable genetic elements.

Transposons and genome evolution in plants

“…Although the transposons that McClintock identified and studied were DNA transposons, both gypsy-like and copia-like retrotransposons were soon identified in the maize genome and subsequently in many other plant genomes (27)(28)(29)(30)(31)(32). It has also become evident that non-long terminal repeat (LTR) retrotransposons are abundant in maize, as well as other plant genomes (33,34).…”

Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium

“…Evidence of a deletional bias among organisms with smaller versus larger genomes (Bennett and Leitch 1997;Petrov and Hartl 1997;Kirik et al 2000;Petrov et al 2000) has led to the "mutational equilibrium model" of DNA loss (Petrov 2002b). Other suggested mechanisms of DNA loss include unequal intrastrand homologous recombination between two tandem repeats in the same orientation, such as the LTRs of retrotransposable elements (Shepherd et al 1984;SanMiguel et al 1996;Chen et al 1998;Vicient et al 1999;, illegitimate recombination (Devos et al 2002;Wicker et al 2003;Ma et al 2004;Bennetzen et al 2005), and double-stranded break repair (Kirik et al 2000;Orel and Puchta 2003;Filkowski et al 2004).…”

Identification and characterization of two tandem repeat sequences (TrsB and TrsC) and a retrotransposon (RIRE1) as genome-general sequences in rice.

“…Besides the ribosomal RNA genes and microsatellite DNA, various kinds of tandem repeat sequences have been found in Secale cereale (Bedbrook et al, 1980;Appels et al, 1986), Arabidopsis thaliana (Martinez-Zapater et al, 1986), Avena sativa (Fabijanski et al, 1990), Oryza sativa (Wu and Wu, 1987;Ohtsubo et al, 1991;De Kochko et al, 1991), and Actinidia deliciosa (Crowhurst and Gardner, 1991). Interspersed sequences identified are various kinds of elements, such as transposable DNA elements (Nevers et al, 1986;Peterson, 1987;Coen et al, 1989;Fedoroff, 1989;Gierl and Saedler, 1992), retrotransposons (Flavell et al, 1992;Moore et al, 1991;Voytas et al, 1992;Hirochika and Hirochika, 1993) and retroposons (Shepherd at al., 1984;Mochizuki et al, 1992;Yoshioka et al, 1993;Deragon et al, 1994).…”