Chloroplast genome sequencing of the medicinal plant Flueggea suffruticosa and phylogenetic analysis of Phyllanthaceae

Flueggea suffruticosa (Pall.) Baill. (Phyllanthaceae) is a medicinally significant shrub in traditional medicine, yet its genomic resources remain scarce. In this study, we reported the first complete chloroplast genome of F. suffruticosa , assembled de novo from Illumina sequencing data. The 157,521 bp genome exhibited a typical quadripartite structure, consisting of two inverted repeats (26,082 bp each), a large single-copy region (86,561 bp), and a small single-copy region (18,796 bp). It encoded 112 unique genes, including 78 protein-coding, 30 tRNA, and 4 rRNA genes. Codon usage was biased toward A/T, with leucine being the most abundant and cysteine the least frequent amino acid. Phylogenomic analysis of 78 shared protein-coding genes from 28 Phyllanthaceae species resolved several well-supported tribal clades. Flueggea suffruticosa formed a robust subclade with two accessions of Flueggea virosa (Roxb. ex Willd.) Royle within Phyllantheae. Notably, Phyllanthus L. was found to be polyphyletic due to the nested positions of Breynia J.R.Forst. & G.Forst. and Glochidion J.R.Forst. & G.Forst., reaffirming the long-standing taxonomic complexities within the tribe. The complete chloroplast genome of F. suffruticosa offers a valuable genomic resource for future evolutionary, phylogenetic, and conservation studies within Flueggea and the broader Phyllanthaceae family.