Foundational genomic resources for date palm (Phoenix dactylifera): A gap-free, telomere-to-telomere phased assembly of Ajwa and 19 high-quality genome assemblies
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 updated, corrected chromosome assemblies validated through cytogenetics, Hi-C and optical mapping. Chromosome numbering was revised based on average lengths across all sequenced genomes. The Sex Determination Region (SDR) was inferred on chromosome 14, spanning approximately 15.2 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 fundamental resource for advancing breeding strategies aimed at enhancing the genetic resilience and productivity of date palm.
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BibTeX
@article{celii2026foundational,
title = {{Foundational genomic resources for date palm (Phoenix dactylifera): A gap-free, telomere-to-telomere phased assembly of Ajwa and 19 high-quality genome assemblies}},
author = {Mirko Celii and Noor Al-Bader and Nahed Mohammed and Yong Zhou and Alice Fornasiero and Maria Navarrete Rodriguez and Raghad Shuwaikan and Umair Ali Toor and Victor Llaca and Kevin Fengler and Praveena Parakkal and Dal-Hoe Koo and Muriel Gros-Balthazard and Vincent Battesti and Thiago Capote and Michael Purugganan and Joel A. Malek and Ikram Blilou and Jesse Poland and Rod Wing},
journal = {Scientific Data},
year = {2026},
month = aug,
doi = {10.1038/s41597-026-08193-0},
url = {https://hal.science/hal-05440322v1},
note = {CC BY-NC-SA 4.0},
}
RIS
TY - JOUR
TI - Foundational genomic resources for date palm (Phoenix dactylifera): A gap-free, telomere-to-telomere phased assembly of Ajwa and 19 high-quality genome assemblies
AU - Mirko Celii
AU - Noor Al-Bader
AU - Nahed Mohammed
AU - Yong Zhou
AU - Alice Fornasiero
AU - Maria Navarrete Rodriguez
AU - Raghad Shuwaikan
AU - Umair Ali Toor
AU - Victor Llaca
AU - Kevin Fengler
AU - Praveena Parakkal
AU - Dal-Hoe Koo
AU - Muriel Gros-Balthazard
AU - Vincent Battesti
AU - Thiago Capote
AU - Michael Purugganan
AU - Joel A. Malek
AU - Ikram Blilou
AU - Jesse Poland
AU - Rod Wing
PY - 2026
DA - 2026/08/31
JO - Scientific Data
DO - 10.1038/s41597-026-08193-0
UR - https://hal.science/hal-05440322v1
AB - 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 updated, corrected chromosome assemblies validated through cytogenetics, Hi-C and optical mapping. Chromosome numbering was revised based on average lengths across all sequenced genomes. The Sex Determination Region (SDR) was inferred on chromosome 14, spanning approximately 15.2 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 fundamental resource for advancing breeding strategies aimed at enhancing the genetic resilience and productivity of date palm.
SN - 2052-4463
ER -