Structure and evolution of theCinfulretrotransposon family of maize

Abstract

A maize cDNA clone was isolated by virtue of its intense hybridization to total maize genomic DNA, indicating homology to highly repetitive sequences. Genomic homologues were identified and subcloned from an adh1-bearing maize yeast artificial chromosome (YAC). Sequencing revealed that the expressed sequence was part of a Ty3-gypsy-type retrotransposon. We discovered and sequenced two complete retrotransposons of this family, and named them Cinful elements because they are members of a family of maize retrotransposons including Zeon-1 and the first plant transposable element sequenced, the solo long terminal repeat (LTR) called Cin1. All are defective, as Cinful-1 and Cinful-2 elements lack gag and Zeon-1 lacks pol homology. Despite the apparent lack of an intact "autonomous" element, the Cinful family has expanded to a copy number of about 18 000, representing just under 9% of the maize genome. Both point mutations and major rearrangements, including possible gene acquisition, differentiate members of the Cinful family. Cinful family members were found to have an unusual feature that we also observed in two other Ty3-class retrotransposons of teosinte and tobacco: related tandem repeats that separate their internal domains with a gag- or pol-containing homology from a 3' segment of unknown function. The conserved and variable features identified provide insights into the origin, mutational history, and functional components of this major constituent of the maize genome.

Retand: a novel family of gypsy-like retrotransposons harboring an amplified tandem repeat

“…Tandem repeats could serve as a junction between an internal domain containing gag-pol and its 3Ј end part containing ORFs with unknown function in the location of retroviral env gene. A similar organization was recently observed in Cinful retrotransposon family (Sanz-Alferez et al 2003).…”

“…So far, the arrays of tandem repeats were found in several mobile elements. They are located upstream of the right LTR in maize retrotransposons Grande1 (Martinez-Izquierdo et al 1997) and Cinful (Sanz-Alferez et al 2003), and Drosophila retrotransposon micropia (Lankenau et al 1994). A special group represents retrotransposons containing the arrays of tandem repeats but lacking coding capacity.…”

“…In addition to Dasheng in rice (Jiang et al 2002a), it includes, e.g., ZLRS element from maize (Monfort et al 1995). So far, no exact function has been attributed to the tandem repeats present in retrotransposones, although their conserved location among some Ty3/gypsy elements indicates their potential structural or functional signiWcance (MartinezIzquierdo et al 1997;Sanz-Alferez et al 2003;Lankenau et al 1994). In order to test their potential to form secondary structures, we performed an analysis using Mfold software (Zuker 2003) for both Retand-1 and Retand-2 tandem repeat arrays as well as for some other tandem repeats located inside mobile elements, including micropia and Grande1.…”

Ogre elements — A distinct group of plant Ty3/gypsy-like retrotransposons

“…-confidence). Sanz-Alferez et al, 2003;Kejnovský et al, 2006). However, origin and eventual function of these repeats are unknown.…”

Genetic diversity and gene flow in six accessions of Meso-America teosintes

“…The genus Zea has a native distribution from Mexico to Nicaragua, a region known as MesoAmerica, and studies on teosinte species may contribute to our understanding of maize genetics (Lukens and Doebley 1999;Evans and Kermicle 2001), molecular population genetics (Guat et al 2000), genome evolution (Sanz-Alferez et al 2003), and crop evolution (Doebley 1990a). Moreover, since F1 hybrids between teosinte and maize are fertile, all teosinte species can potentially contribute to maize breeding, acting as sources of traits such as resistance or tolerance to heavy metals in the soil and other adverse environmental conditions (Dale 1994).…”