Mangrove tree (Avicennia marina): insight into chloroplast genome evolutionary divergence and its comparison with related species from family Acanthaceae

Abstract

Avicennia marina (family Acanthaceae) is a halotolerant woody shrub that grows wildly and cultivated in the coastal regions. Despite its importance, the species suffers from lack of genomic datasets to improve its taxonomy and phylogenetic placement across the related species. Here, we have aimed to sequence the plastid genome of A. marina and its comparison with related species in family Acanthaceae. Detailed next-generation sequencing and analysis showed a complete chloroplast genome of 150,279 bp, comprising 38.6% GC. Genome architecture is quadripartite revealing large single copy (82,522 bp), small single copy (17,523 bp), and pair of inverted repeats (25,117 bp). Furthermore, the genome contains 132 different genes, including 87 protein-coding genes, 8 rRNA, 37 tRNA genes, and 126 simple sequence repeats (122 mononucleotide, 2 dinucleotides, and 2 trinucleotides). Interestingly, about 25 forward, 15 reversed and 14 palindromic repeats were also found in the A. marina. High degree synteny was observed in the pairwise alignment with related genomes. The chloroplast genome comparative assessment showed a high degree of sequence similarity in coding regions and varying divergence in the intergenic spacers among ten Acanthaceae species. The pairwise distance showed that A. marina exhibited the highest divergence (0.084) with Justicia flava and showed lowest divergence with Aphelandra knappiae (0.059). Current genomic datasets are a valuable resource for investigating the population and evolutionary genetics of family Acanthaceae members' specifically A. marina and related species.

Figure 1

Gene map of the Avicennia marina chloroplast genome. Genes drawn inside the circle are transcribed clockwise, and those outside the circle are transcribed counterclockwise. The stars indicate the intron-containing genes. Genes belonging to different functional groups are colour-coded. The darker grey in the inner circle corresponds to GC content, and the lighter grey corresponds to AT content.

Figure 2

Heatmap of pairwise gene divergence in the chloroplast genome sequence of A. marina. The highly divergent genes are represented with light and green color depending on the divergence frequency.

Figure 3

Simple sequence repeats (SSRs) analysis in the chloroplast genome of A. marina. (A) Numbers of SSR types in complete chloroplast genome, (B) Number of SSRs in LSC, IR and SSC regions. (C) frequency of SSR motifs.

Figure 4

Distribution and frequency analysis of repeated sequences in chloroplast genome of A. marina. (A) total number of forward, palindromic and tandem repeats. (B) distribution of palindromic repeats in different ranges of length. (C) distribution of forward repeats in different ranges of length. (D) distribution of tandem repeats in different ranges of length.

Figure 5

Distance between the adjacent genes and junctions of Large single Copy (LSC), two inverted repeats (IR) and Small Single Copy (SSC) in A. marina and 10 other related species. boxes below and above the lines represent the genes located on the border of LSC, IR and SSC. The figure represents the changes in the length and location of certain genes across these borders.

Figure 6

Phylogenetic trees were constructed for twenty-four species from four families using three different methods maximum likelihood (ML), maximum parsimony (MP) and neighbor -joining (NJ) by using 65 shared genes. Numbers above the branches are the bootstrap values of ML, MP and NJ respectively. Red star represents the position for Avicennia marina.