Characteristics and Phylogenetic Analysis of the Complete Chloroplast Genome of Hibiscus sabdariffa L.

Roselle (<i>Hibiscus sabdariffa</i> L.) is a plant rich in bioactive constituents, serving as a unique material for the food and beverage industry and therapeutic applications. Despite its significant utility, few studies have focused on the molecular breeding of the plant. Chloroplasts are organelles in plant cells with independent genetic information, making them ideal for investigating plant phylogeny and genetic evolution. In this study, the roselle breeding material 'Zhe Xiao Luo 1' was selected to assemble and analyze the entire chloroplast genome using the Illumina NovaSeq X Plus platform. The phylogenetic relationships between roselle and other species within Malvaceae family, particularly within the genus Hibiscus, were clarified. The results showed that the complete chloroplast genome of roselle was 162,428 bp in length, with nucleotide proportions of 31.14% (A), 18.73% (C), 18.01% (G), 32.12% (T), and 36.74% (GC). It exhibited a typical tetrad structure consisting of four segments: the large single copy (LSC) region (90,327 bp), the small single-copy (SSC) region (19,617 bp), and two inverted repeat sequences (IRa and IRb, each 26,242 bp). A total of 130 genes were identified, including 37 tRNA genes, 8 rRNA genes, and 85 mRNA genes, and no pseudogenes were detected. Phylogenetic analysis using 23 revealed a clear phylogenetic relationship between <i>H. sabdariffa</i> and <i>H. esculentus</i> (okra) among all tested species. Building on previous research, this study further explored the functional annotation of genes in the roselle chloroplast genome, as well as its codon preference, repetitive sequences, simple sequence repeats (SSR), Ka/Ks ratio, nucleotide diversity (pi) analysis, and boundary analysis. The complete gene sequences have been uploaded to the NCBI database (accession number PX363576). This study provides evidence for elucidating the phylogenetic relationships and taxonomic status of <i>H. sabdariffa</i>, laying a theoretical foundation for studies on molecular mechanism resolution and cultivar development.