The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass, Cenchrus ciliaris
Cenchrus ciliaris is an apomictic, allotetraploid pasture grass widely distributed in the tropical and subtropical regions of Africa and Asia. In this study, we aimed to investigate the genomic organization and characterize some of the repetitive DNA sequences in this species. Due to the apomictic p...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-09-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.952968/full |
| _version_ | 1811261866800840704 |
|---|---|
| author | Priyanka Rathore Priyanka Rathore Trude Schwarzacher Trude Schwarzacher Trude Schwarzacher J. S. Heslop-Harrison J. S. Heslop-Harrison J. S. Heslop-Harrison Vishnu Bhat Paulina Tomaszewska Paulina Tomaszewska |
| author_facet | Priyanka Rathore Priyanka Rathore Trude Schwarzacher Trude Schwarzacher Trude Schwarzacher J. S. Heslop-Harrison J. S. Heslop-Harrison J. S. Heslop-Harrison Vishnu Bhat Paulina Tomaszewska Paulina Tomaszewska |
| author_sort | Priyanka Rathore |
| collection | DOAJ |
| description | Cenchrus ciliaris is an apomictic, allotetraploid pasture grass widely distributed in the tropical and subtropical regions of Africa and Asia. In this study, we aimed to investigate the genomic organization and characterize some of the repetitive DNA sequences in this species. Due to the apomictic propagation, various aneuploid genotypes are found, and here, we analyzed a 2n = 4x + 3 = 39 accession. The physical mapping of Ty1-copia and Ty3-gypsy retroelements through fluorescence in situ hybridization with a global assessment of 5-methylcytosine DNA methylation through immunostaining revealed the genome-wide distribution pattern of retroelements and their association with DNA methylation. Approximately one-third of Ty1-copia sites overlapped or spanned centromeric DAPI-positive heterochromatin, while the centromeric regions and arms of some chromosomes were labeled with Ty3-gypsy. Most of the retroelement sites overlapped with 5-methylcytosine signals, except for some Ty3-gypsy on the arms of chromosomes, which did not overlap with anti-5-mC signals. Universal retrotransposon probes did not distinguish genomes of C. ciliaris showing signals in pericentromeric regions of all 39 chromosomes, unlike highly abundant repetitive DNA motifs found in survey genome sequences of C. ciliaris using graph-based clustering. The probes developed from RepeatExplorer clusters gave strong in situ hybridization signals, mostly in pericentromeric regions of about half of the chromosomes, and we suggested that they differentiate the two ancestral genomes in the allotetraploid C. ciliaris, likely having different repeat sequence variants amplified before the genomes came together in the tetraploid. |
| first_indexed | 2024-04-12T19:13:35Z |
| format | Article |
| id | doaj.art-6680993ad3564339b8f9ca93cb1e453d |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-12T19:13:35Z |
| publishDate | 2022-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-6680993ad3564339b8f9ca93cb1e453d2022-12-22T03:19:48ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-09-011310.3389/fpls.2022.952968952968The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass, Cenchrus ciliarisPriyanka Rathore0Priyanka Rathore1Trude Schwarzacher2Trude Schwarzacher3Trude Schwarzacher4J. S. Heslop-Harrison5J. S. Heslop-Harrison6J. S. Heslop-Harrison7Vishnu Bhat8Paulina Tomaszewska9Paulina Tomaszewska10Department of Botany, Faculty of Science, University of Delhi, New Delhi, IndiaDepartment of Genetics and Genome Biology, University of Leicester, Leicester, United KingdomDepartment of Genetics and Genome Biology, University of Leicester, Leicester, United KingdomKey Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangzhou, ChinaKey Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, ChinaDepartment of Genetics and Genome Biology, University of Leicester, Leicester, United KingdomKey Laboratory of Plant Resources Conservation and Sustainable Utilization, Guangzhou, ChinaKey Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, ChinaDepartment of Botany, Faculty of Science, University of Delhi, New Delhi, IndiaDepartment of Genetics and Genome Biology, University of Leicester, Leicester, United KingdomDepartment of Genetics and Cell Physiology, Faculty of Biological Sciences, University of Wrocław, Wrocław, PolandCenchrus ciliaris is an apomictic, allotetraploid pasture grass widely distributed in the tropical and subtropical regions of Africa and Asia. In this study, we aimed to investigate the genomic organization and characterize some of the repetitive DNA sequences in this species. Due to the apomictic propagation, various aneuploid genotypes are found, and here, we analyzed a 2n = 4x + 3 = 39 accession. The physical mapping of Ty1-copia and Ty3-gypsy retroelements through fluorescence in situ hybridization with a global assessment of 5-methylcytosine DNA methylation through immunostaining revealed the genome-wide distribution pattern of retroelements and their association with DNA methylation. Approximately one-third of Ty1-copia sites overlapped or spanned centromeric DAPI-positive heterochromatin, while the centromeric regions and arms of some chromosomes were labeled with Ty3-gypsy. Most of the retroelement sites overlapped with 5-methylcytosine signals, except for some Ty3-gypsy on the arms of chromosomes, which did not overlap with anti-5-mC signals. Universal retrotransposon probes did not distinguish genomes of C. ciliaris showing signals in pericentromeric regions of all 39 chromosomes, unlike highly abundant repetitive DNA motifs found in survey genome sequences of C. ciliaris using graph-based clustering. The probes developed from RepeatExplorer clusters gave strong in situ hybridization signals, mostly in pericentromeric regions of about half of the chromosomes, and we suggested that they differentiate the two ancestral genomes in the allotetraploid C. ciliaris, likely having different repeat sequence variants amplified before the genomes came together in the tetraploid.https://www.frontiersin.org/articles/10.3389/fpls.2022.952968/fullrepetitive DNAmethylationretrotransposonschromosomespolyploidyaneuploidy |
| spellingShingle | Priyanka Rathore Priyanka Rathore Trude Schwarzacher Trude Schwarzacher Trude Schwarzacher J. S. Heslop-Harrison J. S. Heslop-Harrison J. S. Heslop-Harrison Vishnu Bhat Paulina Tomaszewska Paulina Tomaszewska The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass, Cenchrus ciliaris Frontiers in Plant Science repetitive DNA methylation retrotransposons chromosomes polyploidy aneuploidy |
| title | The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass, Cenchrus ciliaris |
| title_full | The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass, Cenchrus ciliaris |
| title_fullStr | The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass, Cenchrus ciliaris |
| title_full_unstemmed | The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass, Cenchrus ciliaris |
| title_short | The repetitive DNA sequence landscape and DNA methylation in chromosomes of an apomictic tropical forage grass, Cenchrus ciliaris |
| title_sort | repetitive dna sequence landscape and dna methylation in chromosomes of an apomictic tropical forage grass cenchrus ciliaris |
| topic | repetitive DNA methylation retrotransposons chromosomes polyploidy aneuploidy |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.952968/full |
| work_keys_str_mv | AT priyankarathore therepetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT priyankarathore therepetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT trudeschwarzacher therepetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT trudeschwarzacher therepetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT trudeschwarzacher therepetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT jsheslopharrison therepetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT jsheslopharrison therepetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT jsheslopharrison therepetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT vishnubhat therepetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT paulinatomaszewska therepetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT paulinatomaszewska therepetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT priyankarathore repetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT priyankarathore repetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT trudeschwarzacher repetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT trudeschwarzacher repetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT trudeschwarzacher repetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT jsheslopharrison repetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT jsheslopharrison repetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT jsheslopharrison repetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT vishnubhat repetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT paulinatomaszewska repetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris AT paulinatomaszewska repetitivednasequencelandscapeanddnamethylationinchromosomesofanapomictictropicalforagegrasscenchrusciliaris |