Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta)
Cassava (Manihot esculenta Crantz) is a vital tropical root crop providing essential dietary energy to over 800 million people in tropical and subtropical regions. As a climate-resilient crop, its significance grows as the human population expands. However, yield improvement faces challenges from bi...
| Autores principales: | , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2023
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/139946 |
| _version_ | 1855525261398769664 |
|---|---|
| author | Landi, M. Shah, T. Falquet, L. Niazi, A. Stavolone, L. Bongcam-Rudloff, E. Gisel, A. |
| author_browse | Bongcam-Rudloff, E. Falquet, L. Gisel, A. Landi, M. Niazi, A. Shah, T. Stavolone, L. |
| author_facet | Landi, M. Shah, T. Falquet, L. Niazi, A. Stavolone, L. Bongcam-Rudloff, E. Gisel, A. |
| author_sort | Landi, M. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Cassava (Manihot esculenta Crantz) is a vital tropical root crop providing essential dietary energy to over 800 million people in tropical and subtropical regions. As a climate-resilient crop, its significance grows as the human population expands. However, yield improvement faces challenges from biotic and abiotic stress and limited breeding. Advanced sequencing and assembly techniques enabled the generation of a highly accurate, nearly complete, haplotype-resolved genome of the African cassava cultivar TMEB117. It is the most accurate cassava genome sequence to date with a base-level accuracy of QV > 64, N50 > 35 Mbp, and 98.9% BUSCO completeness. Over 60% of the genome comprises repetitive elements. We predicted over 45,000 gene models for both haplotypes. This achievement offers valuable insights into the heterozygosity genome organization of the cassava genome, with improved accuracy, completeness, and phased genomes. Due to its high susceptibility to African Cassava Mosaic Virus (ACMV) infections compared to other cassava varieties, TMEB117 provides an ideal reference for studying virus resistance mechanisms, including epigenetic variations and smallRNA expressions. |
| format | Journal Article |
| id | CGSpace139946 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace1399462025-11-11T10:17:13Z Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta) Landi, M. Shah, T. Falquet, L. Niazi, A. Stavolone, L. Bongcam-Rudloff, E. Gisel, A. cassava cultivars african cassava mosaic virus genomes Cassava (Manihot esculenta Crantz) is a vital tropical root crop providing essential dietary energy to over 800 million people in tropical and subtropical regions. As a climate-resilient crop, its significance grows as the human population expands. However, yield improvement faces challenges from biotic and abiotic stress and limited breeding. Advanced sequencing and assembly techniques enabled the generation of a highly accurate, nearly complete, haplotype-resolved genome of the African cassava cultivar TMEB117. It is the most accurate cassava genome sequence to date with a base-level accuracy of QV > 64, N50 > 35 Mbp, and 98.9% BUSCO completeness. Over 60% of the genome comprises repetitive elements. We predicted over 45,000 gene models for both haplotypes. This achievement offers valuable insights into the heterozygosity genome organization of the cassava genome, with improved accuracy, completeness, and phased genomes. Due to its high susceptibility to African Cassava Mosaic Virus (ACMV) infections compared to other cassava varieties, TMEB117 provides an ideal reference for studying virus resistance mechanisms, including epigenetic variations and smallRNA expressions. 2023 2024-03-13T08:16:01Z 2024-03-13T08:16:01Z Journal Article https://hdl.handle.net/10568/139946 en Open Access application/pdf Springer Landi, M., Shah, T., Falquet, L., Niazi, A., Stavolone, L., Bongcam-Rudloff, E. & Gisel, A. (2023). Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta). Scientific Data, 10(1): 887, 1-9. |
| spellingShingle | cassava cultivars african cassava mosaic virus genomes Landi, M. Shah, T. Falquet, L. Niazi, A. Stavolone, L. Bongcam-Rudloff, E. Gisel, A. Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta) |
| title | Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta) |
| title_full | Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta) |
| title_fullStr | Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta) |
| title_full_unstemmed | Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta) |
| title_short | Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta) |
| title_sort | haplotype resolved genome of heterozygous african cassava cultivar tmeb117 manihot esculenta |
| topic | cassava cultivars african cassava mosaic virus genomes |
| url | https://hdl.handle.net/10568/139946 |
| work_keys_str_mv | AT landim haplotyperesolvedgenomeofheterozygousafricancassavacultivartmeb117manihotesculenta AT shaht haplotyperesolvedgenomeofheterozygousafricancassavacultivartmeb117manihotesculenta AT falquetl haplotyperesolvedgenomeofheterozygousafricancassavacultivartmeb117manihotesculenta AT niazia haplotyperesolvedgenomeofheterozygousafricancassavacultivartmeb117manihotesculenta AT stavolonel haplotyperesolvedgenomeofheterozygousafricancassavacultivartmeb117manihotesculenta AT bongcamrudloffe haplotyperesolvedgenomeofheterozygousafricancassavacultivartmeb117manihotesculenta AT gisela haplotyperesolvedgenomeofheterozygousafricancassavacultivartmeb117manihotesculenta |