Sequencing of Complete Chloroplast Genomes and Comparative Analyses of Codon Usage Bias and Phylogeny in <i>Globba</i> Species

ABSTRACT The genus Globba (Zingiberaceae) comprises over 100 species distributed worldwide, with a primary concentration in Southeast Asia. These plants are of significant interest due to their distinctive and delicate floral morphology as well as their potential medicinal value. In this study, we assembled and characterized the complete chloroplast (cp) genomes of three species: Globba racemosa, G. “Mermaid Princess,” and G. “Ziyan” . Each genome displayed the typical angiosperm quadripartite structure, with total lengths of 163,141 bp, 163,487 bp, and 163,535 bp, respectively. Genome annotation identified 133–134 unique genes, comprising 87 protein‐coding genes, 38–39 tRNAs, and 8 rRNAs. Annotation and comparative analysis of a total of 11 Globba chloroplast genomes revealed that the trnG‐GCC gene was present in two copies exclusively in G. multiflora and G. racemosa , while the trnQ‐UUG gene was specifically absent from the chloroplast genome of G. atrosanguinea . Comparative genomic analysis indicated high synteny across all genomes, with no large‐scale structural rearrangements detected; however, variations at the inverted repeat (IR) boundaries involving the ycf1 and ndhF genes were observed. Codon usage bias analysis demonstrated a strong preference for A/U‐ending codons (RSCU &gt; 1.0), with leucine (Leu), threonine (Thr), and arginine (Arg) being the most frequently encoded amino acids, and 17 optimal codons were identified. Simple sequence repeat (SSR) analysis showed that the total number of SSRs per genome ranged from 60 to 70. Combined analyses of ENC‐plot, PR2‐plot, Neutral‐plot, and BUSTED indicated that codon usage patterns in Globba chloroplast genomes are primarily shaped by mutation pressure. Phylogenetic reconstruction based on 11 complete chloroplast genome sequences revealed that all species were monophyletically grouped into two primary clades. These newly generated cp genomes provide valuable genomic resources for enhancing phylogenetic resolution, elucidating molecular evolutionary patterns, informing conservation strategies, and supporting further research on ornamental and medicinal plants within Globba .