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.

Uncovering the first complete plastome genomics, comparative analyses, and phylogenetic dispositions of endemic medicinal plant Ziziphus hajarensis (Rhamnaceae)

“…Similarly,the rbc L gene was found with the highest pairwise sequence divergence followed by pet N gene. Comparable findings for these genes have previously been reported [ 26 , 47 , 48 ], and our results are supported by Yang et al [ 49 ] suggesting that similar variations exist among different coding regions. These findings are also supported by earlier report that these divergent genes are primarily found in LSC regions and are evolving rapidly [ 47 ].…”

Genetic and molecular mechanisms underlying mangrove adaptations to intertidal environments

“…Vierh. 147,909 88,331 17,772 20,903 112 78 30 4 38.15 ( Li et al., 2020a ) 150,279 82,552 17,523 25,117 132 87 37 8 38.6 ( Asaf et al., 2021 ) 152,288 83,088 17,924 25,638 133 88 37 8 39 ( Shi et al, 2020 ) Lumnitzera littorea (Jack) Voigt. 159,687 88,323 18,558 26,403 130 85 37 8 37.01 ( Zhang et al., 2020c ) Lumnitzera racemosa Willd.…”

“…The evolutionary significance of the loss of infA is yet to be determined. Photosynthesis I and II, cytochrome b 6/f complex, ATP synthase, and Rubisco along with small and large subunit proteins such as ribosomal protein S (rps) and ribosomal protein L (rpl) are annotated from A. marina chloroplast genome ( Asaf et al., 2021 ). Another ribosomal protein gene, rpl7 from the members of Rhizophoraceae ( R. mangle , B. sexangula , R. stylosa , and K. obovata ) is reported to show signs of positive selection ( Han et al., 2020 ).…”

A Regional Review of Marine and Coastal Impacts of Climate Change on the ROPME Sea Area

“…The extent of mangroves, the only evergreen forests in the RSA, has increased in some areas of the UAE and Saudi Arabia particularly thanks to conservation and re-plantation projects, although mangrove cover across the wider RSA remains fragmented and scattered [7,150,181,183,189]. Research on the RSA mangroves has grown exponentially in recent years [191], with studies focusing on the adaptive potential of regional mangroves for informing potential climate change responses globally [195,196].…”