Foundational genomic resources for date palm: A gap-free, telomere-to-telomere phased assembly of Ajwa and 19 high-quality genome assemblies of <i>Phoenix dactylifera</i>
Abstract Phoenix dactylifera L. is an economically, nutritionally, and culturally important fruit crop in the arid and semi-arid regions of the Middle East and North Africa. Here, we present a gap-free, telomere-to-telomere reference genome of the variety Ajwa, along with 19 additional high-quality assemblies (18 female and 1 male). These assemblies reveal novel chromosomal structures validated through cytogenetics, Hi-C, optical mapping, and synteny analyses with other palm genomes. Chromosome names were revised based on average lengths across all sequenced genomes. The Sex Determination Region (SDR) on chromosome 14 was confirmed through male-specific k-mer analysis, spanning approximately 14.7 Mb. Nucleolar organizing regions (NORs) were localized on chromosome 10, where a large 45S rDNA locus displayed unique repeat spacer motifs containing transposon-like sequences. In some accessions, a second NOR was identified on the female sex chromosome. This collection of date palm assemblies, anchored by the Ajwa reference genome, provides a critical resource for advancing breeding strategies aimed at enhancing the genetic resilience and productivity of date palm.
Authors
- Rod A. Wing (ORCID: https://orcid.org/0000-0001-6633-6226)
- Kevin Fengler (ORCID: https://orcid.org/0000-0003-0010-2093)
- Muriel Gros‐Balthazard (ORCID: https://orcid.org/0000-0002-2587-3946)
- Raghad Shuwaikan
- Vincent Battesti (ORCID: https://orcid.org/0000-0002-5793-1098)
- Mirko Celii (ORCID: https://orcid.org/0000-0001-9179-5758)
- Nahed Mohammed (ORCID: https://orcid.org/0000-0002-8857-3246)
- Noor Al-Bader (ORCID: https://orcid.org/0000-0002-0511-6972)
- Jesse Poland (ORCID: https://orcid.org/0000-0002-7856-1399)
- Joel A. Malek (ORCID: https://orcid.org/0000-0002-1516-8477)
- Ikram Blilou (ORCID: https://orcid.org/0000-0001-8003-3782)
- Alice Fornasiero (ORCID: https://orcid.org/0000-0001-6165-4233)
- Jun Hong
- Umair Toor
- Maria Navarrete Rodriguez
- Dal-Hoe Koo
- Michael Purugganan
- Yong Zhou
- Victor Llaca
- Thiago Capote
Institutions
- Centre National de la Recherche Scientifique (FR)
- University of Arizona (US)
- Kansas State University (US)
- Université de Montpellier (FR)
- Université Paris Cité (FR)
- Cornell University (US)
- Diversité, adaptation et développement des plantes (FR)
- Corteva (United States) (US)
- Weill Cornell Medical College in Qatar (QA)
- Musée de l'Homme (FR)
- Institut de Recherche pour le Développement (FR)
- New York University (US)
- King Abdullah University of Science and Technology (SA)
Publication Details
- Journal
- bioRxiv (Cold Spring Harbor Laboratory)
- Published
- 2025-12-31
- DOI
- https://doi.org/10.64898/2025.12.30.696066
- Primary Topic
- Chromosomal and Genetic Variations
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- King Abdullah University of Science and Technology