Haplotype-resolved genome assembly of the tetraploid potato cultivar Désirée
Abstract Cultivar Désirée is an important model for potato functional genomics studies to assist breeding strategies. Here, we present a haplotype-resolved genome assembly of Désirée, achieved by assembling PacBio HiFi reads and Hi-C scaffolding, resulting in a high-contiguity chromosome-level assem...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-06-01
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| Series: | Scientific Data |
| Online Access: | https://doi.org/10.1038/s41597-025-05372-3 |
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| author | Tim Godec Sebastian Beier Natalia Yaneth Rodriguez-Granados Rashmi Sasidharan Lamis Abdelhakim Markus Teige Björn Usadel Kristina Gruden Marko Petek |
| author_facet | Tim Godec Sebastian Beier Natalia Yaneth Rodriguez-Granados Rashmi Sasidharan Lamis Abdelhakim Markus Teige Björn Usadel Kristina Gruden Marko Petek |
| author_sort | Tim Godec |
| collection | DOAJ |
| description | Abstract Cultivar Désirée is an important model for potato functional genomics studies to assist breeding strategies. Here, we present a haplotype-resolved genome assembly of Désirée, achieved by assembling PacBio HiFi reads and Hi-C scaffolding, resulting in a high-contiguity chromosome-level assembly. We implemented a comprehensive annotation pipeline incorporating gene models and functional annotations from the Solanum tuberosum Phureja DM reference genome alongside RNA-seq reads to provide high-quality gene and transcript annotations. Additionally, we provide a genome-wide DNA methylation profile using Oxford Nanopore reads, enabling insights into potato epigenetics. The assembled genome, annotations, methylation and expression data are visualised in a publicly accessible genome browser, providing a valuable resource for the potato research community. |
| format | Article |
| id | doaj-art-8cc57cd2a2da4176a183b97fe9ee2ef8 |
| institution | Kabale University |
| issn | 2052-4463 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Data |
| spelling | doaj-art-8cc57cd2a2da4176a183b97fe9ee2ef82025-08-20T03:47:24ZengNature PortfolioScientific Data2052-44632025-06-011211810.1038/s41597-025-05372-3Haplotype-resolved genome assembly of the tetraploid potato cultivar DésiréeTim Godec0Sebastian Beier1Natalia Yaneth Rodriguez-Granados2Rashmi Sasidharan3Lamis Abdelhakim4Markus Teige5Björn Usadel6Kristina Gruden7Marko Petek8National Institute of Biology, Department of Biotechnology and Systems BiologyInstitute of Bio- and Geosciences (IBG-4 Bioinformatics), Bioeconomy Science Center (BioSC), CEPLAS, Forschungszentrum Jülich GmbHPlant Stress Resilience, Institute of Environmental Biology, Utrecht UniversityPlant Stress Resilience, Institute of Environmental Biology, Utrecht UniversityPSI (Photon Systems Instruments)Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University ViennaInstitute of Bio- and Geosciences (IBG-4 Bioinformatics), Bioeconomy Science Center (BioSC), CEPLAS, Forschungszentrum Jülich GmbHNational Institute of Biology, Department of Biotechnology and Systems BiologyNational Institute of Biology, Department of Biotechnology and Systems BiologyAbstract Cultivar Désirée is an important model for potato functional genomics studies to assist breeding strategies. Here, we present a haplotype-resolved genome assembly of Désirée, achieved by assembling PacBio HiFi reads and Hi-C scaffolding, resulting in a high-contiguity chromosome-level assembly. We implemented a comprehensive annotation pipeline incorporating gene models and functional annotations from the Solanum tuberosum Phureja DM reference genome alongside RNA-seq reads to provide high-quality gene and transcript annotations. Additionally, we provide a genome-wide DNA methylation profile using Oxford Nanopore reads, enabling insights into potato epigenetics. The assembled genome, annotations, methylation and expression data are visualised in a publicly accessible genome browser, providing a valuable resource for the potato research community.https://doi.org/10.1038/s41597-025-05372-3 |
| spellingShingle | Tim Godec Sebastian Beier Natalia Yaneth Rodriguez-Granados Rashmi Sasidharan Lamis Abdelhakim Markus Teige Björn Usadel Kristina Gruden Marko Petek Haplotype-resolved genome assembly of the tetraploid potato cultivar Désirée Scientific Data |
| title | Haplotype-resolved genome assembly of the tetraploid potato cultivar Désirée |
| title_full | Haplotype-resolved genome assembly of the tetraploid potato cultivar Désirée |
| title_fullStr | Haplotype-resolved genome assembly of the tetraploid potato cultivar Désirée |
| title_full_unstemmed | Haplotype-resolved genome assembly of the tetraploid potato cultivar Désirée |
| title_short | Haplotype-resolved genome assembly of the tetraploid potato cultivar Désirée |
| title_sort | haplotype resolved genome assembly of the tetraploid potato cultivar desiree |
| url | https://doi.org/10.1038/s41597-025-05372-3 |
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