Complete Chloroplast Genomes of Vachellia nilotica and Senegalia senegal: Comparative Genomics and Phylogenomic Placement in a New Generic System

Abstract

Vachellia and Senegalia are the most important genera in the subfamily Mimosoideae (Fabaceae). Recently, species from both genera were separated from the long-characterized Acacia due to their macro-morphological characteristics. However, this morpho-taxonomic differentiation struggles to discriminate some species, for example, Vachellia nilotica and Senegalia senegal. Therefore, sequencing the chloroplast (cp) genomes of these species and determining their phylogenetic placement via conserved genes may help to validate the taxonomy. Hence, we sequenced the cp genomes of V. nilotica and S. senegal, and the results showed that the sizes of the genomes are 165.3 and 162.7 kb, respectively. The cp genomes of both species comprised large single-copy regions (93,849~91,791 bp) and pairs of inverted repeats (IR; 26,093~26,008 bp). The total numbers of genes found in the V. nilotica and S. senegal cp genomes were 135 and 132, respectively. Approximately 123:130 repeats and 290:281 simple sequence repeats were found in the S. senegal and V. nilotica cp genomes, respectively. Genomic characterization was undertaken by comparing these genomes with those of 17 species belonging to related genera in Fabaceae. A phylogenetic analysis of the whole genome dataset and 56 shared genes was undertaken by generating cladograms with the same topologies and placing both species in a new generic system. These results support the likelihood of identifying segregate genera from Acacia with phylogenomic disposition of both V. nilotica and S. senegal in the subfamily Mimosoideae. The current study is the first to obtain complete genomic information on both species and may help to elucidate the genome architecture of these species and evaluate the genetic diversity among species.

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.

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.