De novo assembled nuclear, chloroplast, and mitochondrial genomes show high intraspecific variation in the tropical rainforest species Symphonia globulifera.

Symphonia globulifera (Clusiaceae) has emerged as a model organism in tropical forest ecology and evolution due to its significant ecological role and complex biogeographical history. Originating from Africa, this species has independently colonized Caribbean, Central, and South America three times, becoming a key component of tropical ecosystems across these regions. Despite the ecological importance of S. globulifera and other tropical tree species, our understanding of their genomic architecture remains limited compared to temperate species. To bridge this gap, we present a comparative analysis of two de novo assembled nuclear genomes of S. globulifera-one from a South American individual and one from an African individual-and report newly assembled chloroplast and mitochondrial genomes. Initial assembly of the organelles was performed using GetOrganelle, and the results were compared with corresponding publicly available sequences from closely related Garcinia species. Our study introduces novel genomic resources, including an annotated nuclear draft genome based on Illumina short reads, the first chloroplast genome assembly for the genus, and a set of assembled mitochondrial gene sequences. Additionally, we provide a set of single-copy nuclear gene alignments identified by BUSCO as well as manually curated coding plastid genes, which will serve as valuable tools for future comparative analyses and phylogenetic studies. Our preliminary results based on chloroplast genes and limited sampling suggest that Garcinia might be nonmonophyletic. The detected differences in nuclear and organellar genomes reveal high intraspecific variation, emphasizing the importance of genome-wide sampling for understanding tropical tree evolution.