Genome-wide comparison reveals large structural variants in cassava landraces
Background Structural variants (SVs) are critical for plant genomic diversity and phenotypic variation. This study investigates a large, 9.7 Mbp highly repetitive segment on chromosome 12 of TMEB117, a region not previously characterized in cassava (Manihot esculenta Crantz). We aim to explore its p...
| Main Authors: | , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
2025
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/174535 |
| _version_ | 1855534511718137856 |
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| author | Landi, M. Carluccio, A.V. Shah, T. Niazi, A. Stavolone, L. Falquet, L. Gisel, A. Bongcam-Rudloff, E. |
| author_browse | Bongcam-Rudloff, E. Carluccio, A.V. Falquet, L. Gisel, A. Landi, M. Niazi, A. Shah, T. Stavolone, L. |
| author_facet | Landi, M. Carluccio, A.V. Shah, T. Niazi, A. Stavolone, L. Falquet, L. Gisel, A. Bongcam-Rudloff, E. |
| author_sort | Landi, M. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Background
Structural variants (SVs) are critical for plant genomic diversity and phenotypic variation. This study investigates a large, 9.7 Mbp highly repetitive segment on chromosome 12 of TMEB117, a region not previously characterized in cassava (Manihot esculenta Crantz). We aim to explore its presence and variability across multiple cassava landraces, providing insights into its genomic significance and potential implications.
Results
We validated the presence of the 9.7 Mbp segment in the TMEB117 genome, distinguishing it from other published cassava genome assemblies. By mapping short-read sequencing data from 16 cassava landraces to TMEB117 chromosome 12, we observed variability in read mapping, suggesting that while all genotypes contain the insertion region, some exhibit missing segments or sequence differences. Further analysis revealed two unique genes associated with deacetylase activity, HDA14 and SRT2, within the insertion. Additionally, the MUDR-Mutator transposable element was significantly overrepresented in this region.
Conclusions
This study uncovers a large structural variant in the TMEB117 cassava genome, highlighting its variability among different genotypes. The enrichment of HDA14 and SRT2 genes and the MUDR-Mutator elements within the insertion suggests potential functional significance, though further research is needed to explore this. These findings provide important insights into the role of structural variations in shaping cassava genomic diversity. |
| format | Journal Article |
| id | CGSpace174535 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2025 |
| publishDateRange | 2025 |
| publishDateSort | 2025 |
| record_format | dspace |
| spelling | CGSpace1745352025-11-11T10:40:35Z Genome-wide comparison reveals large structural variants in cassava landraces Landi, M. Carluccio, A.V. Shah, T. Niazi, A. Stavolone, L. Falquet, L. Gisel, A. Bongcam-Rudloff, E. cassava variants manihot esculenta chromosomes dna Background Structural variants (SVs) are critical for plant genomic diversity and phenotypic variation. This study investigates a large, 9.7 Mbp highly repetitive segment on chromosome 12 of TMEB117, a region not previously characterized in cassava (Manihot esculenta Crantz). We aim to explore its presence and variability across multiple cassava landraces, providing insights into its genomic significance and potential implications. Results We validated the presence of the 9.7 Mbp segment in the TMEB117 genome, distinguishing it from other published cassava genome assemblies. By mapping short-read sequencing data from 16 cassava landraces to TMEB117 chromosome 12, we observed variability in read mapping, suggesting that while all genotypes contain the insertion region, some exhibit missing segments or sequence differences. Further analysis revealed two unique genes associated with deacetylase activity, HDA14 and SRT2, within the insertion. Additionally, the MUDR-Mutator transposable element was significantly overrepresented in this region. Conclusions This study uncovers a large structural variant in the TMEB117 cassava genome, highlighting its variability among different genotypes. The enrichment of HDA14 and SRT2 genes and the MUDR-Mutator elements within the insertion suggests potential functional significance, though further research is needed to explore this. These findings provide important insights into the role of structural variations in shaping cassava genomic diversity. 2025 2025-05-13T08:33:47Z 2025-05-13T08:33:47Z Journal Article https://hdl.handle.net/10568/174535 en Open Access application/pdf Landi, M., Carluccio, A.V., Shah, T., Niazi, A., Stavolone, L., Falquet, L., ... & Bongcam-Rudloff, E. (2025). Genome-wide comparison reveals large structural variants in cassava landraces. BMC genomics, 26(1): 362, 1-13. |
| spellingShingle | cassava variants manihot esculenta chromosomes dna Landi, M. Carluccio, A.V. Shah, T. Niazi, A. Stavolone, L. Falquet, L. Gisel, A. Bongcam-Rudloff, E. Genome-wide comparison reveals large structural variants in cassava landraces |
| title | Genome-wide comparison reveals large structural variants in cassava landraces |
| title_full | Genome-wide comparison reveals large structural variants in cassava landraces |
| title_fullStr | Genome-wide comparison reveals large structural variants in cassava landraces |
| title_full_unstemmed | Genome-wide comparison reveals large structural variants in cassava landraces |
| title_short | Genome-wide comparison reveals large structural variants in cassava landraces |
| title_sort | genome wide comparison reveals large structural variants in cassava landraces |
| topic | cassava variants manihot esculenta chromosomes dna |
| url | https://hdl.handle.net/10568/174535 |
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