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 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 basis lags behind that of temperate species. To bridge this gap, we present the full-genome comparison of two de novo-assembled S. globulifera nuclear genomes from a South American and an African individual, and compare chloroplast and mitochondrial genomes to the corresponding sequences from closely related Garcinia species. Our study introduces novel genomic resources, including an annotated draft genome, the first chloroplast genome assembly for the genus, and a set of assembled mitochondrial genes. Additionally, we provide a set of single-copy nuclear gene alignments as well as manually curated coding plastid genes, which will serve as valuable tools for future comparative analyses and phylogenetic studies. Our results based on chloroplast genes suggest that Garcinia is non-monophyletic as it should also include S. globulifera. These findings enhance our understanding of intraspecific genetic variation in tropical trees and contribute to the broader field of tropical ecology and evolutionary biology.