Haplotype-resolved genome assembly of the tetraploid potato cultivar Désirée

Tim Godec; Sebastian Beier; Natalia Yaneth Rodriguez-Granados; Rashmi Sasidharan; Lamis Abdelhakim; Markus Teige; Björn Usadel; Kristina Gruden; Marko Petek

doi:10.1038/s41597-025-05372-3

Haplotype-resolved genome assembly of the tetraploid potato cultivar Désirée

Tim Godec
, Sebastian Beier
, Natalia Yaneth Rodriguez-Granados
, Rashmi Sasidharan
, Lamis Abdelhakim
, Markus Teige
, Björn Usadel
, Kristina Gruden
, Marko Petek

Veröffentlichungen: Beitrag in Fachzeitschrift › Artikel › Peer Reviewed

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.

Originalsprache	Englisch
Aufsatznummer	1044
Fachzeitschrift	Scientific Data
Jahrgang	12
Ausgabenummer	1
DOIs	https://doi.org/10.1038/s41597-025-05372-3
Publikationsstatus	Veröffentlicht - 20 Juni 2025

Fördermittel

This work benefits from resources and services provided by ELIXIR, a distributed infrastructure for life science data, funded by national governments and the European Commission, particularly the Elixir-SI node for performing Illumina paired-end sequencing. Funding for this work was provided by the European Union’s Horizon 2020 research and innovation programme projects ADAPT (grant agreement ID 862858) and UNTWIST (grant agreement ID 862524), Slovenian Research and Innovation Agency (ARIS) project grants P4-0165, P4-0431, and J4-3089. SB and BU are supported by the German Federal Ministry of Education and Research (BMBF) in the frame of the German Network for Bioinformatics Infrastructure (de.NBI).

ÖFOS 2012

106014 Genomik

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10.1038/s41597-025-05372-3

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abstract = "Cultivar D{\'e}sir{\'e}e is an important model for potato functional genomics studies to assist breeding strategies. Here, we present a haplotype-resolved genome assembly of D{\'e}sir{\'e}e, 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.",

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AU - Godec, Tim

AU - Beier, Sebastian

AU - Rodriguez-Granados, Natalia Yaneth

AU - Sasidharan, Rashmi

AU - Abdelhakim, Lamis

AU - Teige, Markus

AU - Usadel, Björn

AU - Gruden, Kristina

AU - Petek, Marko

N1 - Publisher Copyright: © The Author(s) 2025.

PY - 2025/6/20

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N2 - 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.

AB - 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.

KW - Solanum tuberosum/genetics

KW - Genome, Plant

KW - Haplotypes

KW - Tetraploidy

KW - DNA Methylation

KW - Molecular Sequence Annotation

UR - https://www.scopus.com/pages/publications/105008764640

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DO - 10.1038/s41597-025-05372-3

M3 - Article

C2 - 40541992

SN - 2052-4463

VL - 12

JO - Scientific Data

JF - Scientific Data

IS - 1

M1 - 1044

ER -

Haplotype-resolved genome assembly of the tetraploid potato cultivar Désirée

Abstract

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ÖFOS 2012

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