Comprehensive re-assembly and annotation dataset for the argan tree (Argania spinosa L., Sapotaceae) genome

We present a comprehensive annotation dataset for the scaffold-level nuclear genome assembly of the argan tree (Argania spinosa (L.) Skeels, Sapotaceae). Using Illumina whole-genome shotgun reads that we previously generated for the "Argan Amghar" individual and deposited under BioProject PRJNA294096, together with the corresponding GenBank assembly GCA_003260245.2, we re-assembled and curated a 690 Mbp draft with scaffold N50 of 25 Mbp and L50 of 11 large macro-scaffolds. Ab initio gene prediction with AUGUSTUS and GeneMark-ES, integrated by EVidenceModeler, produced 51,078 protein-coding genes and 2,081 non-coding RNA genes, while repeat annotation covers 53.0% of the assembly. Functional annotation combined eggNOG-mapper, InterProScan and BLASTp searches against UniProtKB/Swiss-Prot to assign curated functions, domains and Gene Ontology terms to 32,785 genes and to support 25,484 proteins with UniProt evidence. BUSCO analyses indicate high completeness of the assembly gene space and completeness of the predicted proteome (74.6%). All primary data products, including a unified GFF3 file and the predicted proteome FASTA, are openly available via NCBI and Zenodo ( https://doi.org/10.5281/zenodo.17901083 ).