Complete chloroplast genome sequence of Gynostemma guangxiense: genome structure, codon usage bias, and phylogenetic relationships in Gynostemma (Cucurbitaceae)

Gynostemma guangxiense X.X.Chen & D.H.Qin is an important medicinal species distributed in Guangxi, China. In this study, we obtained the complete chloroplast (cp) genome sequence for G. guangxiense using Illumina paired-end sequencing technology and analyzed the codon usage pattern with bioinformatics approaches. The cp genome of G. guangxiense comprises 157,785 bp with a pair of inverted repeat regions (26,288 bp) separated by one large single copy region (86,702 bp) and one small single copy region (18,507 bp). The whole genome contains 130 unique genes, where 113 are unique, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. In addition, 62 repeats and 70 simple sequence repeats were identified. Phylogenetic inference based on 73 protein-coding genes indicated that G. guangxiense has a close relationship with Gynostemma caulopterum S.Z. He. In addition, 52 CDSs longer than 300 bp in the G. guangxiense cp genome were screened to analyze synonymous codon usage. The neutrality plot indicated a weak correlation between GC₁₂ and GC₃. Effective number of codons plot analysis showed that most genes were distributed below the expected curve. PR2-plot mapping analysis revealed that G and T were used more frequently than C and A at the third base position. Finally, 16 codons were identified as the optimal codons. These findings suggest that natural selection has mainly influenced codon usage in the G. guangxiense cp genome. The results obtained in this study of G. guangxiense provide an important theoretical basis for its molecular identification, utilization, and conservation.