That this 6-mer occurs so abundantly in many of the stable H2A/H4R3me2s nucleosomal DNA sequences is suggestive of it being a repetitive element, or component thereof – an observation we explore in downstream analysis.
This is a particularly challenging problem since all such telomeres have a core repetitive component called X (≈ 475 bp long) as well as several combinatorial repeats and sometimes a larger repetitive component (see Saccharomyces Genome Database, www.yeastgenome.org).org
In terms of the challenging goal of a reference pine genome sequence, this predominance of a highly diverged repetitive component is critical since large amounts of identical dispersed repeats are inevitable sources of gaps in an assembly.
The aim of the present study is to verify the suitability of using different approaches of de novo assembling sequence reads obtained by NGS procedures (Illumina and 454) to gain a comprehensive characterization of the repetitive component of a plant species (Helianthus annuus), whose large-sized genome is being sequenced thanks to the efforts of an international sequencing consortium [ 21, 34].
Bertioli, D.J. et al. The repetitive component of the A genome of peanut (Arachis hypogaea) and its role in remodelling intergenic sequence space since its evolutionary divergence from the B genome.
Now that a characterization of the repetitive component of sunflower has been achieved, it is important to analyze variation in the relative proportion of the LTR-RTs among genotypes, cultivars, and wild accessions of the genus Helianthus.
The OLEAREP database, made of 83,324 repetitive contigs, gives a precise characterization of the repetitive component of the O. europaea genome.
Changes in the repetitive component of a genome may influence all kinds of significant phenomena, from gene expression to genome size.
In the frame of a project aiming to obtain the complete sequence of the olive genome, we performed a deep analysis of the repetitive component of this genome, using NGS techniques (454-Roche and Illumina).
Secondly, the method used to isolate full-length REs allowed us to select especially dispersed elements, whereas nested elements were probably under-represented in the sample, and it is known that nested REs constitute a large fraction of the repetitive component in medium- to large-sized genomes, such as those of maize or sunflower.
A larger effort to characterize the repetitive component of the sunflower genome was then made by analyzing approximately 25% of the genome from 454 random sequence reads [ 21].
