Comparative analysis of DNA repeats and identification of novel Fesreba centromeric element in fescues and ryegrasses
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.
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Posted 13 May, 2020
On 17 Jun, 2020
Received 21 May, 2020
Received 11 May, 2020
On 01 May, 2020
On 29 Apr, 2020
Invitations sent on 29 Apr, 2020
On 29 Apr, 2020
On 28 Apr, 2020
On 20 Feb, 2020
On 15 Apr, 2020
Received 14 Apr, 2020
On 31 Mar, 2020
Received 21 Mar, 2020
On 09 Mar, 2020
Invitations sent on 06 Mar, 2020
On 03 Mar, 2020
On 21 Feb, 2020
On 21 Feb, 2020
Comparative analysis of DNA repeats and identification of novel Fesreba centromeric element in fescues and ryegrasses
Posted 13 May, 2020
On 17 Jun, 2020
Received 21 May, 2020
Received 11 May, 2020
On 01 May, 2020
On 29 Apr, 2020
Invitations sent on 29 Apr, 2020
On 29 Apr, 2020
On 28 Apr, 2020
On 20 Feb, 2020
On 15 Apr, 2020
Received 14 Apr, 2020
On 31 Mar, 2020
Received 21 Mar, 2020
On 09 Mar, 2020
Invitations sent on 06 Mar, 2020
On 03 Mar, 2020
On 21 Feb, 2020
On 21 Feb, 2020
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