The Complete Chloroplast Genome of Bruguiera gymnorhiza (L.) Lam (Rhizophoraceae): Genome Structure and Phylogenetic Relationships

Background: Bruguiera gymnorhiza (L.) Lam is an ecologically important true mangrove species in the family Rhizophoraceae, widely distributed across tropical and subtropical coastlines. Despite its broad range, genomic resources for this species, particularly for populations in Vietnam, remain scarce. Chloroplast genomes (cp genomes) provide essential information for understanding plastome evolution, phylogenetic relationships, and conservation genetics in mangrove plants. Methods: We sequenced the complete cp genome of B. gymnorhiza (VN-DU) from Vietnam using Illumina high-throughput technology. The plastome was assembled and annotated, followed by analyses of genome architecture, gene content, intron organization, codon usage, and simple sequence repeats (SSRs). Phylogenetic relationships were reconstructed using maximum likelihood and Bayesian inference based on complete cp genomes from representative Rhizophoraceae species. Results: The cp genome of B. gymnorhiza (VN-DU) is 163,780 bp in length and exhibits the typical quadripartite structure comprising a large single-copy, small single-copy, and two identical inverted repeats (IRs). Genome structure and gene order were highly conserved relative to other mangrove species. A total of 104 SSRs were identified, predominantly A/T-rich motifs located mainly in noncoding regions. Codon usage analysis revealed a strong preference for A/U-ending codons. Phylogenetic analyses consistently placed the Vietnamese accession within a strongly supported Bruguiera clade. Conclusions: This study provides the first complete cp genome of B. gymnorhiza from Vietnam, offering a valuable reference for plastome evolution, phylogenetic studies, and conservation genetics of Rhizophoraceae mangroves.