Complete Chloroplast Genome of Curculigo orchioides from Vietnam: Structural Features, Repeat Signatures, and High-Resolution Candidate DNA Barcodes

Thi Ha Dang, Phu Nguyen and Van Hoang

Background and Objective: Curculigo orchioides is a valuable medicinal plant that has been overexploited in Vietnam, leading to a significant decline in its genetic resources. The chloroplast genome, characterized by high structural conservation, provides a reliable framework for species identification and phylogenetic inference. This study aimed to characterize the complete chloroplast genome of C. orchioides collected in Vietnam and to evaluate its structural features, sequence variation, and phylogenetic position. Materials and Methods: Raw sequencing reads were quality-filtered using fastp v1.3.1, assembled with GetOrganelle, and annotated via CPGAVAS2. Repetitive elements were identified using MISA and REPuter/EMBOSS. Codon usage bias was assessed based on GC3s, ENc, CAI, Fop, and CBI indices. Genome alignment and nucleotide diversity (π) analyses were conducted using MAFFT, and phylogenetic relationships were reconstructed with IQ-TREE. Results: The chloroplast genome is approximately 157 kb in length and displays a typical quadripartite circular structure, comprising 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. A total of 48 simple sequence repeats (SSRs), predominantly A/T mononucleotide motifs, and nine long sequence repeats (LSRs) were detected, indicating overall structural stability. Codon usage analysis revealed a strong A/T bias (low GC3s) and evidence of translational optimization in genes related to the genetic machinery, notably rps18 with a high CAI value. A hypervariable region (≈118-140 kb) with elevated nucleotide diversity was identified around rpoC2, representing a promising candidate for high-resolution DNA barcoding. Phylogenomic analysis confirmed that the Vietnamese accession forms a well-supported monophyletic clade with C. orchioides and is closely related to Hypoxis. Conclusion: These findings provide genomic resources for provenance tracing and phylogenetic studies within Hypoxidaceae.

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