Comparative analyses of DNA repeats and identification of a novel Fesreba centromeric element in fescues and ryegrasses
Abstract 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 tetra...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2020-06-01
|
| Series: | BMC Plant Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12870-020-02495-0 |
| _version_ | 1818836048756604928 |
|---|---|
| author | Jana Zwyrtková Alžběta Němečková Jana Čížková Kateřina Holušová Veronika Kapustová Radim Svačina David Kopecký Bradley John Till Jaroslav Doležel Eva Hřibová |
| author_facet | Jana Zwyrtková Alžběta Němečková Jana Čížková Kateřina Holušová Veronika Kapustová Radim Svačina David Kopecký Bradley John Till Jaroslav Doležel Eva Hřibová |
| author_sort | Jana Zwyrtková |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-19T03:00:25Z |
| format | Article |
| id | doaj.art-b5fb342fcc3a496292c2ffddfd8bbe8c |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-19T03:00:25Z |
| publishDate | 2020-06-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-b5fb342fcc3a496292c2ffddfd8bbe8c2022-12-21T20:38:13ZengBMCBMC Plant Biology1471-22292020-06-0120111510.1186/s12870-020-02495-0Comparative analyses of DNA repeats and identification of a novel Fesreba centromeric element in fescues and ryegrassesJana Zwyrtková0Alžběta Němečková1Jana Čížková2Kateřina Holušová3Veronika Kapustová4Radim Svačina5David Kopecký6Bradley John Till7Jaroslav Doležel8Eva Hřibová9Institute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural ResearchCentro de Genómica Nutricional AgroacuícolaInstitute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany, Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural ResearchAbstract 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.http://link.springer.com/article/10.1186/s12870-020-02495-0FestucaLoliumIllumina sequencingRepetitive DNACentromere organization |
| spellingShingle | Jana Zwyrtková Alžběta Němečková Jana Čížková Kateřina Holušová Veronika Kapustová Radim Svačina David Kopecký Bradley John Till Jaroslav Doležel Eva Hřibová Comparative analyses of DNA repeats and identification of a novel Fesreba centromeric element in fescues and ryegrasses BMC Plant Biology Festuca Lolium Illumina sequencing Repetitive DNA Centromere organization |
| title | Comparative analyses of DNA repeats and identification of a novel Fesreba centromeric element in fescues and ryegrasses |
| title_full | Comparative analyses of DNA repeats and identification of a novel Fesreba centromeric element in fescues and ryegrasses |
| title_fullStr | Comparative analyses of DNA repeats and identification of a novel Fesreba centromeric element in fescues and ryegrasses |
| title_full_unstemmed | Comparative analyses of DNA repeats and identification of a novel Fesreba centromeric element in fescues and ryegrasses |
| title_short | Comparative analyses of DNA repeats and identification of a novel Fesreba centromeric element in fescues and ryegrasses |
| title_sort | comparative analyses of dna repeats and identification of a novel fesreba centromeric element in fescues and ryegrasses |
| topic | Festuca Lolium Illumina sequencing Repetitive DNA Centromere organization |
| url | http://link.springer.com/article/10.1186/s12870-020-02495-0 |
| work_keys_str_mv | AT janazwyrtkova comparativeanalysesofdnarepeatsandidentificationofanovelfesrebacentromericelementinfescuesandryegrasses AT alzbetanemeckova comparativeanalysesofdnarepeatsandidentificationofanovelfesrebacentromericelementinfescuesandryegrasses AT janacizkova comparativeanalysesofdnarepeatsandidentificationofanovelfesrebacentromericelementinfescuesandryegrasses AT katerinaholusova comparativeanalysesofdnarepeatsandidentificationofanovelfesrebacentromericelementinfescuesandryegrasses AT veronikakapustova comparativeanalysesofdnarepeatsandidentificationofanovelfesrebacentromericelementinfescuesandryegrasses AT radimsvacina comparativeanalysesofdnarepeatsandidentificationofanovelfesrebacentromericelementinfescuesandryegrasses AT davidkopecky comparativeanalysesofdnarepeatsandidentificationofanovelfesrebacentromericelementinfescuesandryegrasses AT bradleyjohntill comparativeanalysesofdnarepeatsandidentificationofanovelfesrebacentromericelementinfescuesandryegrasses AT jaroslavdolezel comparativeanalysesofdnarepeatsandidentificationofanovelfesrebacentromericelementinfescuesandryegrasses AT evahribova comparativeanalysesofdnarepeatsandidentificationofanovelfesrebacentromericelementinfescuesandryegrasses |