Diverse patterns of the tandem repeats organization in rye chromosomes

Abstract

Although the monomer size, nucleotide sequence, abundance and species distribution of tandemly organized DNA families are well characterized, little is known about the internal structure of tandem arrays, including total arrays size and the pattern of monomers distribution. Using our rye specific probes, pSc200 and pSc250, we addressed these issues for telomere associated rye heterochromatin where these families are very abundant. Fluorescence in situ hybridization (FISH) on meiotic chromosomes revealed a specific mosaic arrangement of domains for each chromosome arm where either pSc200 or pSc250 predominates without any obvious tendency in order and size of domains. DNA of rye-wheat monosomic additions studied by pulse field gel electrophoresis produced a unique overall blot hybridization display for each of the rye chromosomes. The FISH signals on DNA fibres showed multiple monomer arrangement patterns of both repetitive families as well as of the Arabidopsis-type telomere repeat. The majority of the arrays consisted of the monomers of both families in different patterns separated by spacers. The primary structure of some spacer sequences revealed scrambled regions of similarity to various known repetitive elements. This level of complexity in the long-range organization of tandem arrays has not been previously reported for any plant species. The various patterns of internal structure of the tandem arrays are likely to have resulted from evolutionary interplay, array homogenization and the generation of heterogeneity mediated by double-strand breaks and associated repair mechanisms.

Evolutionary dynamics and sites of illegitimate recombination revealed in the interspersion and sequence junctions of two nonhomologous satellite DNAs in cactophilic Drosophila species

“…In contrast, there are only few data sets about the structure and organization of satDNA arrays at the molecular level (Shiels et al, 1997;Zinic et al, 2000;Alkhimova et al, 2004;Lee et al, 2006). It remains to be investigated whether the interspersion noted here is a regular occurrence or associated to some peculiar features of the Drosophila microchromosomes, such as highly heterochromatic nature, suppressed meiotic recombination and presence of few genes (reviewed by Riddle and Elgin, 2006), allowing a more complex interplay between satDNAs without deleterious effects.…”

“…Interspersion of nonhomologous satellites is rarely reported, although was observed between the pSc200 and pSc250 satellites in subtelomeric regions of rye chromosomes (Alkhimova et al, 2004).…”

“…In the 'copy-choice' model, illegitimate recombination can occur during DNA replication, when the polymerization of a new DNA strand is interrupted at certain sites and continues at a different template position. Such slippage events can be facilitated by the presence of palindrome sequences forming secondary structures, such as that found in one of the junctions between satellites pSc200 and pSc250 in rye (Alkhimova et al, 2004).…”

“…Whole-genome projects have many sharp junctions of satellites with generally uncharacterized genomic DNA, although accurate assembly of individual sequence reads into satDNA arrays may be extremely difficult (see Lee et al, 2006 for care required for assembly of blocks of HORs). Nevertheless, in examples that have been verified, abrupt transitions involving satDNA Â satDNA or satDNA Â defined non-satDNA junctions have been reported in a number of organisms, such as humans (Gaff et al, 1994), plants (Alkhimova et al, 2004;Lee et al, 2006) and insects (McAllister and Werren, 1999;Sun et al, 2003;Krzywinski et al, 2005).…”

Characterization of the Arachis (Leguminosae) D genome using fluorescence in situ hybridization (FISH) chromosome markers and total genome DNA hybridization

“…Dot blot analysis in plants relies largely on the hybridization of genome repetitive sequences since they are a major component of genomes. Rapid evolution of those sequences can lead to changes in sequence motif and/or abundance of a particular sequence even between narrowly related species (Schmidt and Heslop-Harrison, 1998;Alkhimova et al, 2004), without being necessarily related to changes in the gross karyotype morphology (Ugarkovic and Plohl, 2002). This fact may explain, at least in part, the incongruence between molecular and chromosome data, reflecting differences in the rate and direction of evolution at each level.…”