Fig 1.
Genome map of the Vachellia nilotica and Senegalia senegal chloroplast genome.
Thick lines indicate the extent of the inverted repeat regions (IRa and IRb), which separate the genome into small (SSC) and large (LSC) single copy regions. Genes drawn inside the circle are transcribed clockwise, and those outside are transcribed counterclockwise. Genes belonging to different functional groups are color-coded. The dark grey in the inner circle corresponds to the GC content, and the light grey corresponds to the AT content.
Table 1.
Composition of Vachellia nilotica and Senegalia senegal cp genomes with related species.
Table 2.
Genes in the sequenced V. nilotica and S. senegal species chloroplast genomes.
Table 3.
Base composition of the Vachellia nilotica and Senegalia senegal chloroplast genome.
Fig 2.
Analysis of repeated sequences in V. nilotica and S. senegal.
(A) Totals of three repeat types, (B) Frequency of palindromic repeats by length, (C) Frequency of forward repeats by length and (D) Frequency of tandem repeats by length.
Fig 3.
Analysis of simple sequence repeat (SSR) in V. nilotica and S. senegal genomes with related species cp genomes.
Number of different SSR types detected in these genomes.
Fig 4.
Analysis of simple sequence repeat (SSR) in the V. nilotica and S. senegal genomes.
Frequency of identified SSRs in the Small Single-Copy (SSC), Large Simple-Copy (LSC), Inverted Repeat (IR), transfer RNA (tRNA), ribosomal RNA (rRNA), and coding sequence (CDS) regions.
Fig 5.
Comparison of border distance between adjacent genes and junctions of LSC, SSC and two IR regions among the chloroplast genomes of V. nilotica and S. senegal with related species.
Boxes above or below the main line indicate the adjacent border genes. The figure is not to scale with respect to sequence length and only shows relative changes at or near the IR/SC borders.
Fig 6.
Phylogenetic tree constructed on the basis of whole genome dataset using four different methods: Bayesian inference (BI), maximum likelihood (ML), maximum parsimony (MP), and neighbor-joining (NJ).
Numbers above the branches are the posterior probabilities of BI and bootstrap values for ML, MP and NJ. The star represents the position of V. nilotica and S. senegal.