Luzula elegans shows interplay between centromere and large-scale genome organization

Chromosomes of monocentric species are sub-structured into distinguishable eu- and heterochromatic regions in a genome size depend way at the large scale. To address whether holocentric chromosomes display the same features we characterized the repeated genome fraction by analysis of next generation sequencing data and studied the distribution of eu- and heterochromatin typical chromatin modifications in the holocentric wood-rush Luzula elegans. The highly repetitive DNA fraction of this species represents 61% of the 3.81 Gbp/1C sized haploid genome. None of the 20 identified satellite repeats displayed a distribution pattern reminiscent of the almost chromosome-wide distribution of the centromere in Luzula. Instead, a tendency of satellite clustering at centromere-free chromosome termini was found. Various non-centromeric mobile elements including the most abundant repeat, Angela family of Ty1/copia LTR-retrotransposons (33% of the genome), are dispersed along chromosomes. An interspersed arrangement of euchromatic and heterochromatic domains and of early and late replicating DNA was found at the large scale, while a distinct sub-organization into chromatin subunits was detectable via super-high resolution light microscopy. We speculate that the L. elegans genome consists of multiple DNA sequence-independent centromeric subunits interspersed by non-centromeric subunits. Overall, our data suggests that an interplay exists between centromere organization and a holocentric genome organization at the large scale.