Genome-wide comparison reveals large structural variants in cassava landraces
| cg.authorship.types | CGIAR and advanced research institute | en |
| cg.contributor.affiliation | Swedish University of Agricultural Sciences | en |
| cg.contributor.affiliation | International Institute of Tropical Agriculture | en |
| cg.contributor.affiliation | Institute of Sustainable Plant Protection, Italy | en |
| cg.contributor.affiliation | University of Fribourg | en |
| cg.contributor.crp | Roots, Tubers and Bananas | |
| cg.contributor.donor | Swedish Research Council | en |
| cg.coverage.country | United States | |
| cg.coverage.iso3166-alpha2 | US | |
| cg.coverage.region | ACP | |
| cg.coverage.region | Northern America | |
| cg.creator.identifier | Michael Landi: 0000-0001-5597-7802 | en |
| cg.creator.identifier | Anna Vittoria Carluccio: 0000-0001-6887-5792 | en |
| cg.creator.identifier | Trushar Shah: 0000-0002-0091-7981 | en |
| cg.creator.identifier | LIVIA STAVOLONE: 0000-0002-0691-1302 | en |
| cg.creator.identifier | Laurent Falquet: 0000-0001-8102-7579 | en |
| cg.creator.identifier | ANDREAS GISEL: 0000-0001-7218-9488 | en |
| cg.creator.identifier | Erik Bongcam-Rudloff: 0000-0002-1947-8288 | en |
| cg.howPublished | Formally Published | en |
| cg.identifier.doi | https://doi.org/10.1186/s12864-025-11523-y | en |
| cg.isijournal | ISI Journal | en |
| cg.issn | 1471-2164 | en |
| cg.issue | 1: 362 | en |
| cg.journal | BMC Genomics | en |
| cg.reviewStatus | Peer Review | en |
| cg.subject.iita | AGRONOMY | en |
| cg.subject.iita | CASSAVA | en |
| cg.subject.iita | FOOD SECURITY | en |
| cg.subject.iita | PLANT GENETIC RESOURCES | en |
| cg.subject.sdg | SDG 2 - Zero hunger | en |
| cg.volume | 26 | en |
| dc.contributor.author | Landi, M. | en |
| dc.contributor.author | Carluccio, A.V. | en |
| dc.contributor.author | Shah, T. | en |
| dc.contributor.author | Niazi, A. | en |
| dc.contributor.author | Stavolone, L. | en |
| dc.contributor.author | Falquet, L. | en |
| dc.contributor.author | Gisel, A. | en |
| dc.contributor.author | Bongcam-Rudloff, E. | en |
| dc.date.accessioned | 2025-05-13T08:33:47Z | en |
| dc.date.available | 2025-05-13T08:33:47Z | en |
| dc.identifier.uri | https://hdl.handle.net/10568/174535 | |
| dc.title | Genome-wide comparison reveals large structural variants in cassava landraces | en |
| dcterms.abstract | 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. | en |
| dcterms.accessRights | Open Access | |
| dcterms.audience | Scientists | en |
| dcterms.available | 2025-04-10 | en |
| dcterms.bibliographicCitation | 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. | en |
| dcterms.description | Open Access Journal | en |
| dcterms.extent | 1-13 | en |
| dcterms.issued | 2025 | en |
| dcterms.language | en | |
| dcterms.license | CC-BY-4.0 | |
| dcterms.subject | cassava | en |
| dcterms.subject | variants | en |
| dcterms.subject | manihot esculenta | en |
| dcterms.subject | chromosomes | en |
| dcterms.subject | dna | en |
| dcterms.type | Journal Article |