A Draft Genome Assembly of Argania spinosa Provides Insights into Lipid Metabolism-Associated Genes and Repeat-Rich Genome Architecture

Argania spinosa (L.) Skeels is an ecologically and economically important Moroccan tree valued for its oil-rich seeds and adaptation to arid environments. Here, we generated and characterized a genotype-specific draft genome assembly of Z-AL-IV-13 using approximately 82.7 GB of Illumina sequencing data. The final contamination-screened assembly comprised 584.21 Mb across 139,591 sequences, with an N50 of 6.84 kb. BUSCO analysis identified 59.1% complete, 25.4% fragmented, and 15.6% missing conserved eudicot orthologs, while independent k-mer analyses indicated incomplete genome representation and substantial repetitive sequence. Comparative whole-genome alignments showed that 95.34–97.60% of the represented Z-AL-IV-13 assembly sequence aligned to five published A. spinosa assemblies, indicating high sequence correspondence among represented regions. Protein-supported annotation identified 44,777 transcript models, of which 37,507 (83.77%) produced significant Swiss-Prot matches. RepeatMasker identified 37.73% of the assembly as repetitive, predominantly unclassified interspersed repeats. Targeted homology analyses identified assembly loci associated with fatty-acid and triacylglycerol metabolism, including ACCase components, KAS, SACPD, FAD2, GPAT, LPAT/LPAAT, DGAT, PDAT, and acyl-ACP thioesterase families. These sequence-based assignments identify candidate lipid-metabolism-associated homologs but do not establish pathway completeness, biochemical function, or definitive gene-copy numbers. Overall, Z-AL-IV-13 provides an independently generated, genotype-specific draft genomic resource that complements chromosome-scale A. spinosa references while retaining the limitations associated with assembly fragmentation and incomplete gene-space recovery.