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Data from: Comparative analysis of DNA repeats and identification of novel Fesreba centromeric element in fescues and ryagrasses

Citation

Hribova, Eva (2021), Data from: Comparative analysis of DNA repeats and identification of novel Fesreba centromeric element in fescues and ryagrasses, Dryad, Dataset, https://doi.org/10.5061/dryad.xksn02vch

Abstract

Background
Cultivated grasses are an important source of food for domestic animals worldwide. Better knowledge of their genomes can speed up the development of new cultivars with better quality and resistance to biotic and abiotic stresses. The most widely grown grasses are tetraploid ryegrass species ( Lolium spp.) and diploid and hexaploid fescue species (Festuca spp.). 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.

Results
Partial genome sequences produced by Illumina technology were 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 the most striking differences in copy number 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 repeatome analysis in a set of fescues and ryegrasses provided new insights into their genome organization and divergence, including the assembly of LTR element Fesreba. A new LTR element Fesreba was identified and found abundant in centromeric regions of the fescues and ryegrasses. It may have a role in the function of their centromeres.

Methods

Partial genome sequences produced by Illumina technology were used for genome-wide comparative analyses using RepeatExplorer pipeline. DNA repeat were assembled and further characterized based on the homology searches and other tools useful for repeat characterization (e.g. BLASTN and BLASTX programs, phylogenetic analysis). Tandem organized repeats were identified using Dotter.

Usage Notes

Dataset (multifasta file) contains contigs of DNA repeats identified in ten representatives of fescues and ryegrasses.

Funding

ERDF, Award: CZ.02.1.01/0.0/0.0/16_019/0000827

ERDF, Award: CZ.02.1.01/0.0/0.0/16_019/0000827