Fig 1.
Chloroplast gene maps of Ficus sarmentosa var. sarmentosa, Ficus guizhouensis, and Ficus howii.
Genes drawn inside are transcribed clockwise and genes drawn outside are counterclockwise. Genes belonging to different functional groups are color coded. In the inner circle, dark gray and light gray indicate the GC content and AT content, respectively. The boundaries of the large single copy (LSC), small single copy (SSC), and two inverted regions (IRa, IRb) are also shown in the inner circle.
Table 1.
Summary of complete chloroplast genomes of all thirteen taxa in the F. sarmentosa species complex.
Fig 2.
Comparison of the boundaries between the large single copy (LSC), small single copy (SSC), and two inverted repeat regions (IRs) among 13 chloroplast genomes in the F. sarmentosa complex.
The numbers around the vertical lines indicate the distances between the boundaries and the starting or ending bases of their nearest genes.
Fig 3.
Comparison of long repeat sequences among 13 F. sarmentosa complex genomes.
A, The number of each of four long repeat types (P, palindromic; F, forward; R; reverse; C complement); B, The number of long repeat sequences of different lengths.
Fig 4.
Comparison of simple sequence repeats (SSRs) among 13 F. sarmentosa complex genomes.
A, The number of SSRs containing one- to five-nucleotide motifs; B, The number of different SSR motifs.
Table 2.
The relative synonymous codon usage (RSCU) of all 64 codons.
The taxa are represented by the numbers indicated in Table 1.
Fig 5.
Comparison of complete chloroplast genomes among 13 taxa in the F. sarmentosa complex with F. anserina as a reference.
Thick, gray arrows above the alignment indicate the orientation and position of each gene. A cut-off of 70% identity was chosen for the plots. The Y-axis represents the identity percentage, ranging from 50 to 100%.
Fig 6.
Nucleotide diversity of genes and intergenic spacer regions among 13 taxa in the F. sarmentosa complex.
The alignment lengths are indicated on the bars. The horizontal lines indicate the average nucleotide diversity of genes and intergenic spacer regions, respectively. The top five genes or intergenic spacers with the highest nucleotide diversity are highlighted in blue.
Fig 7.
Boxplot of Ka/Ks ratios for 80 unique CDS regions.
The value 1.0 represents the situation where both Ka and Ks equal zero. The line chart superimposed upon the boxplot demonstrates the frequency of infinite Ka/Ks ratios (Ka > 0 and Ks = 0), with detailed numbers labeled simultaneously.
Fig 8.
The maximum likelihood (ML) phylogenetic tree of 123 chloroplast genomes in Ficus with six Olmedieae genomes as the outgroup.
Only the branches with either SH-aLRT or ultrafast bootstrap < 95% were annotated by corresponding values. The starred tip names indicate genomes obtained from Bruun-Lund et al. [26]; the red names indicate genomes obtained in this study; the blue names indicate members of the F. auriculata complex; and the bold names indicate members of the F. sarmentosa complex. The subgenus and section division of Ficus are annotated to the right of tip names. The topology of the ML tree is shown in the upper left corner (excluding the outgroup).