Characterization of the Complete Chloroplast Genome of Hopea Rudiformis P.S. Ashton, a Critically Endangered and Endemic Tree from Borneo Island

The complete chloroplast genome of Hopea rudiformis, a critically endangered species on the IUCN Red List, was sequenced and analyzed to uncover its genomic structure, gene content, and evolutionary context, contributing essential resources for conservation and phylogenetics. Assembled using GetOrganelle with 146.3x coverage, the plastome spans 151,323 bp and follows the typical quadripartite structure of angiosperms, comprising an LSC, SSC, and two IR regions, with an overall GC content of 37.39%, highest in the IRs due to rRNA gene enrichment. A total of 126 genes were annotated, including 83 protein-coding genes, 35 tRNAs, and 8 rRNAs, with gene losses (infA, ycf15, atpF), intron reductions (clpP, rps12), and the presence of cis- and trans-splicing genes (notably trans-spliced rps12) highlighting structural and functional plastome modifications. Codon usage and amino acid profiles showed biases favoring translational efficiency, while 191 SSRs-primarily trinucleotides-were identified, offering potential for marker development. Comparative genome analysis with other Hopea species (H. odorata, H. hainanensis, and H. dryobalanoides) revealed high synteny and conserved IR boundaries, with minor lineage-specific shifts. Phylogenomic analysis positioned H. rudiformis within a well-supported clade alongside these congeners, confirming its evolutionary placement in the core Hopea lineage. This study not only clarifies the plastid genome architecture of H. rudiformis but also provides a foundation for its genetic conservation, phylogenetic refinement within Dipterocarpaceae, and future biodiversity research.