See the published version of this article at BMC Plant Biology.
This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Comparative analysis of DNA repeats and identification of novel Fesreba centromeric element in fescues and ryegrasses
Eva Hřibová
IEB AS CR
Corresponding Author
ORCiD: https://orcid.org/0000-0002-6868-4344
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Plant Biology.
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.
Keywords
Festuca spp., Lolium spp., Illumina sequencing, repetitive DNA, centromere organization
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8
This is a list of supplementary files associated with this preprint. Click to download.
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 2
Posted 13 May, 2020
Published
On 17 Jun, 2020
No community comments so far
Review #1 received
Received 21 May, 2020
Review #2 received
Received 11 May, 2020
Reviewer #2 agreed
On 01 May, 2020
Editor assigned
On 29 Apr, 2020
Reviewers invited
Invitations sent on 29 Apr, 2020
Reviewer #1 agreed
On 29 Apr, 2020
Editor invited
On 28 Apr, 2020
Submission checks complete
On 20 Feb, 2020
No comments provided
Editorial decision: Minor revision
On 15 Apr, 2020
Review #2 received
Received 14 Apr, 2020
Reviewer #2 agreed
On 31 Mar, 2020
Review #1 received
Received 21 Mar, 2020
Reviewer #1 agreed
On 09 Mar, 2020
Reviewers invited
Invitations sent on 06 Mar, 2020
Editor assigned
On 03 Mar, 2020
Submission checks complete
On 21 Feb, 2020
Editor invited
On 21 Feb, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Plant Molecular Biology and Genetics
Learn more about our company.
This preprint is under consideration at BMC Plant Biology. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Comparative analysis of DNA repeats and identification of novel Fesreba centromeric element in fescues and ryegrasses
Eva Hřibová
IEB AS CR
Corresponding Author
ORCiD: https://orcid.org/0000-0002-6868-4344
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 2
Posted 13 May, 2020
Published
On 17 Jun, 2020
No community comments so far
Review #1 received
Received 21 May, 2020
Review #2 received
Received 11 May, 2020
Reviewer #2 agreed
On 01 May, 2020
Editor assigned
On 29 Apr, 2020
Reviewers invited
Invitations sent on 29 Apr, 2020
Reviewer #1 agreed
On 29 Apr, 2020
Editor invited
On 28 Apr, 2020
Submission checks complete
On 20 Feb, 2020
No comments provided
Editorial decision: Minor revision
On 15 Apr, 2020
Review #2 received
Received 14 Apr, 2020
Reviewer #2 agreed
On 31 Mar, 2020
Review #1 received
Received 21 Mar, 2020
Reviewer #1 agreed
On 09 Mar, 2020
Reviewers invited
Invitations sent on 06 Mar, 2020
Editor assigned
On 03 Mar, 2020
Submission checks complete
On 21 Feb, 2020
Editor invited
On 21 Feb, 2020
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Plant Molecular Biology and Genetics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Plant Biology.
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.
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
Figure 7
Figure 8