TheTy1-copia group retrotransposons ofAllium cepa are distributed throughout the chromosomes but are enriched in the terminal heterochromatin

Abstract

The genomic organization and diversity of the Ty1-copia group retrotransposons has been investigated in a monocotyledonous plant, Allium cepa. We used the polymerase chain reaction (PCR) to generate sequences corresponding to a conserved domain of the reverse transcriptase gene of Ty1-copia retrotransposons in this plant. Sequence analysis of 27 of these PCR products shows that they are a highly heterogeneous population, a feature which is common in plants but not in yeast and Drosophila. Slot-blot analysis shows there are 100,000-200,000 copies of Ty1-copia group retrotransposons within the A. cepa genome (2C = 31.7 pg), indicating that they are a significant component of the genome of this plant. In situ hybridization to metaphase chromosomes reveals that Ty1-copia retrotransposons are distributed throughout the euchromatin of all chromosomes of A. cepa but are enriched in the terminal heterochromatic regions, which contain tandem arrays of satellite sequences. This is the first clear evidence for the presence of Ty1-copia retrotransposons in the terminal heterochromatin of plants and contrasts with the distribution of these elements in other plant species.

Absence of close-facing retrotransposons: A comparison of molecular data and theory

“…Although it would be expected that retrotransposon insertion would be tolerated in non-coding regions of the genome (Bennetzen, 2000;Wicker et al, 2001), in-situ hybridisations show that retroelements are present (with minor exceptions) throughout the entire genome (Pearce et al, 1996b;Waugh et al, 1997). On a finer scale, and in particular where the distribution of individual retroelements is studied in more detail, the distribution of elements is less uniform with extremely high densities of retrotransposons existing in particular genomic locations (Vitte and Panaud, 2005).…”

Assessment of genetic relationships among Secale taxa by using ISSR and IRAP markers and the chromosomal distribution of the AAC microsatellite sequence

“…Retrotransposons are ubiquitous and abundant components of grass genomes, constituting a major fraction of repetitive sequences (approximately 10%-60% of the genome). In many species there is a positive correlation between the copy number of retrotransposons and genome size (Pearce et al, 1996;Vicient et al, 2001;Schulman et al, 2004). It is thought that even among individuals within one population there are differences in copy numbers of a given retrotransposon.…”

Distribution of a Ty3/gypsy-like retroelement on the A and B-chromosomes of Cestrum strigilatum Ruiz & Pav. and Cestrum intermedium Sendtn. (Solanaceae)

“…Besides this general dispersed tendency, both species exhibited a concentration of these elements in some terminal regions, associated with NORs, which are also associated with GC-rich heterochromatin (Fregonezi et al, 2004). Retroelements have previously been reported to be associated with the NORs of some Triticeae (Belyayev et al, 2001), with the heterochromatin of Allium cepa (onion) (Pearce et al, 1996) and A. thaliana , and with centromeric regions in several monocotyledons (Kumar and Bennetzen, 1999) and dicotyledons (Santini et al, 2002). Retrotransposons have also been reported to be associated with the whole genome as segments dispersed along the A-and D-chromosomes of Avena sativa (oat) (Linares et al, 2001).…”