The Complete Chloroplast Genome of Dioscorea hypoglauca: Comparative Genomics and Phylogenetic Insights

The complete chloroplast genome of Dioscorea hypoglauca-a medicinal plant native to southern China-was assembled and characterized. The genome is circular, 153,219 bp in length, and follows the typical quadripartite organization: a large single-copy (LSC) region of 83,692 bp, a small single-copy (SSC) region of 18,813 bp, and two inverted repeat (IR) regions, each 25,357 bp. In total, 129 genes were annotated, including 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Thirty-five simple sequence repeats (SSRs) were detected; most were mononucleotide A/T repeats. A comparison with 22 other Dioscorea species showed that IR boundaries vary considerably across the genus. One notable finding is the boundary shift of the ycf1 gene in D. hypoglauca, which has not been observed in other examined species. Nucleotide diversity (Pi) analysis revealed that intergenic spacers-especially rpl22-rps19 (Pi = 0.11204)-are highly variable, whereas tRNA genes are extremely conserved. Codon usage analysis indicated a strong bias toward A/T-ending codons. Phylogenetic reconstruction based on complete plastomes (using maximum likelihood and Bayesian inference) placed D. hypoglauca as a close relative of D. aspersa and D. pyrifolia. Overall, these results clarify the systematic position of D. hypoglauca, illustrate the dynamic evolution of IR regions within Dioscorea, and provide a genomic resource for future evolutionary and population genetic studies.