Codon bias analysis in the chloroplast genome of Warburgia ugandensis (Canellaceae) and phylogenetic analysis within magnoliids

The complete chloroplast genome of Warburgia ugandensis , an endangered medicinal tree in East Africa, was sequenced and characterized. The genome is 157,374 bp in length with a typical quadripartite structure, comprising a large single-copy region of 87,235 bp, a small single-copy region of 17,873 bp, and two inverted repeats of 26,133 bp each. The overall GC content is 36.5%, and the genome encodes 113 unique genes. Phylogenetic analysis of 74 magnoliid species from five orders and 12 families robustly places W. ugandensis as the earliest-diverging lineage within the order Canellales, forming a sister clade to Tasmannia lanceolata , Drimys granadensis , and Pseudowintera colorata . Codon usage bias analysis reveals pronounced AT-richness and deviation from mutation-driven expectations. Neutrality plot, ENC-plot, and PR2-plot collectively demonstrate that natural selection plays a major role in shaping codon usage patterns. Seven candidate optimal codons, predominantly ending in A or U, were identified. Ka/Ks ratio analysis indicates pervasive purifying selection across most protein-coding genes, with only rpl23 showing a ratio > 1 suggestive of positive selection. RSCU-based clustering and Ka/Ks-based clustering are both consistent with the basal phylogenetic position of this species indicated by the phylogenetic tree. This study provides the first foundational chloroplast genomic resource for W. ugandensis , which may be useful for future conservation genetic studies of this threatened species.