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

0531603 - ÚEB 2021 RIV GB eng J - Článek v odborném periodiku
Zwyrtková, Jana - Němečková, Alžběta - Čížková, Jana - Holušová, Kateřina - Kapustová, Veronika - Svačina, Radim - Kopecký, David - Till, B. J. - Doležel, Jaroslav - Hřibová, Eva
Comparative analyses of DNA repeats and identification of a novel Fesreba centromeric element in fescues and ryegrasses.
BMC Plant Biology. Roč. 20, č. 1 (2020), č. článku 280. ISSN 1471-2229. E-ISSN 1471-2229
Grant CEP: GA MŠMT(CZ) EF16_019/0000827
Institucionální podpora: RVO:61389030
Klíčová slova: Centromere organization * Festuca * Illumina sequencing * Lolium * Repetitive DNA
Obor OECD: Biochemistry and molecular biology
Impakt faktor: 4.215, rok: 2020
Způsob publikování: Open access
http://doi.org/10.1186/s12870-020-02495-0

Background: 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. 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. Results: Partial 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. Conclusions: Comparative 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.
Trvalý link: http://hdl.handle.net/11104/0310235