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Figure 1. 

Gene map of the complete chloroplast genome of A. xanthioides. Genes located on the inside and outside of the circle are transcribed clockwise and counterclockwise, respectively. The inner circle indicates the GC and AT content.

Figure 2. 

Comparison of the borders of the LSC, SSC, and IR regions in the genomes of the three Amomum species. Ψ indicates pseudogenes. The number above the gene feature indicates the distance between the ends of genes and border sites. Figure is not drawn to scale.

Figure 3. 

Codon content of 20 amino acids and stop codons in all protein-coding genes of the chloroplast genomes. The histogram (as read from left to right) shows the different numbers of codons found in A. xanthioides, A. villosum and A. longiligulare.

Figure 4. 

Repeat sequences in three Amomum chloroplast genomes. REPuter was used to identify repeat sequences with length ≥ 30 bp and sequences for which ≥ 90% were identified in chloroplast genomes. Different letters are used to indicate forward repeats (F), palindromic repeats (P), reverse repeats (R), and complementary repeats (C). Repeats of different lengths are indicated in different colors.

Figure 5. 

Sequence alignment in the chloroplast genomes of three Amomum species using mVISTA software. The top line shows the genes in order (with the direction of transcription indicated by an arrow). A cut-off of 70% identity was used for the plots. The Y-axis indicates the value of percent identity and ranges from 50% to 100%.

Figure 6. 

Phylogenetic tree constructed using the maximum likelihood (ML) method based on 53 protein-coding genes from 16 species in the Zingiberales clade. Numbers at nodes indicate the values of bootstrap support.