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

Jana Zwyrtková,Veronika Kapustová,Jaroslav Doležel,Kateřina Holušová,Radim Svačina,Alžběta Němečková,Bradley John Till,David Kopecký,Eva Hřibová

doi:10.1186/s12870-020-02495-0

Abstract

BackgroundCultivated grasses are an important source of food for domestic animals worldwide. Increased knowledge of their genomes can speed up the development of new cultivars with better quality and greater resistance to biotic and abiotic stresses. The most widely grown grasses are tetraploid ryegrass species (Lolium) and diploid and hexaploid fescue species (Festuca). In this work, we characterized repetitive DNA sequences and their contribution to genome size in five fescue and two ryegrass species as well as one fescue and two ryegrass cultivars.ResultsPartial genome sequences produced by Illumina sequencing technology were used for genome-wide comparative analyses with the RepeatExplorer pipeline. Retrotransposons were the most abundant repeat type in all seven grass species. The Athila element of the Ty3/gypsy family showed the most striking differences in copy number between fescues and ryegrasses. The sequence data enabled the assembly of the long terminal repeat (LTR) element Fesreba, which is highly enriched in centromeric and (peri)centromeric regions in all species. A combination of fluorescence in situ hybridization (FISH) with a probe specific to the Fesreba element and immunostaining with centromeric histone H3 (CENH3) antibody showed their co-localization and indicated a possible role of Fesreba in centromere function.ConclusionsComparative repeatome analyses in a set of fescues and ryegrasses provided new insights into their genome organization and divergence, including the assembly of the LTR element Fesreba. A new LTR element Fesreba was identified and found in abundance in centromeric regions of the fescues and ryegrasses. It may play a role in the function of their centromeres.

Highlights

Cultivated grasses are an important source of food for domestic animals worldwide
All histograms of relative Deoxyribonucleic acid (DNA) content represented two dominant peaks corresponding to G1 phase of cell cycle (G1) nuclei of the sample and the standard
The 2C nuclear DNA content determined ranged from 5.32 pg in L. multiflorum to 20.17 pg in F. gigantea

Summary

Introduction

Cultivated grasses are an important source of food for domestic animals worldwide. Increased knowledge of their genomes can speed up the development of new cultivars with better quality and greater resistance to biotic and abiotic stresses. Grasses (Poaceae) are an important source of food for domestic animals worldwide and perform important ecological and environmental functions. Festuca is the largest genus of the family Poaceae, containing more than 600 species, and Torrecilla and Catalán [4] discriminated its two main evolutionary lines: broad leaved and fine leaved (Fig. 1). Broad-leaved Festuca species (hereafter “fescues”) include the subgenus Schedonorus, which gave rise to Lolium species (hereafter “ryegrasses”), a sister group of fescues (Fig. 1) [1]. The species of Loliinae have large genomes ranging from 2.6 Gbp/1C to 11.8 Gbp/1C [7, 8]

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