Comparative analysis of DNA repeats and identification of a Fesreba centromeric element in fescues and ryegrasses

Abstract

Background Cultivated grasses are an important source of food for domestic animals worldwide. Better knowledge of their genomes can speed up development of cultivars with better quality and resistance to biotic and abiotic stresses. The most widely grown grasses are tetraploid ryegrass ( Lolium ) species and diploid and hexaploid fescues ( Festuca ) species. In this work we characterized repetitive DNA sequences and their contribution to genome size in seven fescue and ryegrass species. Results Partial genome sequences were produced by Illumina technology and used for genome-wide comparative analyses using RepeatExplorer pipeline. Retrotransposons were found to be the most abundant repeat types in all seven grass species. Athila element of Ty3/gypsy family showed most striking difference in copy numbers in nuclear genomes between fescues and ryegrasses. The sequence data enabled the assembly of an LTR element Fesreba, which is highly enriched in centromeric and (peri)centromeric regions in all species. A combination of FISH with a probe specific to Fesreba element and immunostaining with CENH3 antibody showed their colocalization and indicated a possible role of Fesreba in centromere function. Conclusions Comparative analysis of repeatome in a set of fescues and ryegrasses provided new insights into their genome organization and divergence, including the assembly of LTR element Fesreba. The element was abundant in centromeric regions of the fescues and ryegrasses and may have a role in function of their centromeres.