A phased, near-telomere-to-telomere chromosome-scale reference genome of the Moroccan argan tree

Abstract

The argan tree (Argania spinosa), endemic to Morocco, holds major ecological and economic value. We generated a high-quality, chromosome-scale, phased reference genome using PacBio HiFi long reads and Hi-C scaffolding. The assembly resolves two haplotypes, each organized into 11 pseudochromosomes (2n = 22). Haplotype-1 spans 621 Mb (scaffold N50 = 50 Mb; GC = 33.79%), and Haplotype-2 spans 615 Mb (scaffold N50 = 51 Mb; GC = 33.77%). BUSCO completeness is 97.8% for Hap1 and 98.1% for Hap2, with Merqury QV values of 75 for both, indicating high consensus accuracy and strong phasing. Telomeric repeats (AAACCCT)n appear at both ends of most chromosomes, and only small terminal gaps remain, so we conservatively classify the assemblies as near-T2T. We annotated 35,183 gene loci producing 39,805 mRNA isoforms and 410 tRNA genes, with 76.46% of loci functionally characterized. Repeats represent 61.65% of the genome, dominated by LTR retrotransposons. All raw data, assemblies, and annotations are publicly accessible, providing a robust genomic foundation for conservation genetics, breeding, and evolutionary studies in A. spinosa.