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

Interspecific variation and phylogenetic relationship between mangrove and non-mangrove species of a same family (Meliaceae)-insights from comparative analysis of complete chloroplast genome

The mahogany family, Meliaceae, contains 58 genera with only one mangrove genus: Xylocarpus. Two of the three species of the genus Xylocarpus are true mangroves (X. granatum and X. moluccensis), and one is a non-mangrove (X. rumphii). In order to resolve the phylogenetic relationship between the mangrove and non-mangrove species, we sequenced chloroplast genomes of these Xylocarpus species along with two non-mangrove species of the Meliaceae family (Carapa guianensis and Swietenia macrophylla) and compared the genome features and variations across the five species. The five Meliaceae species shared 130 genes (85 protein-coding genes, 37 tRNA, and eight rRNA) with identical direction and order, with a few variations in genes and intergenic spacers. The repetitive sequences identified in the rpl22 gene region only occurred in Xylocarpus, while the repetitive sequences in accD were found in X. moluccensis and X. rumphii. The TrnH-GUG and rpl32 gene regions and four non-coding gene regions showed high variabilities between X. granatum and the two non-mangrove species (S. macrophylla and C. guianensis). In addition, among the Xylocarpus species, only two genes (accD and clpP) showed positive selection. Carapa guianensis and S. macrophylla owned unique RNA editing sites. The above genes played an important role in acclimation to different stress factors like heat, low temperature, high UV light, and high salinity. Phylogenetic analysis with 22 species in the order Sapindales supported previous studies, which revealed that the non-mangrove species X. rumphii is closer to X. moluccensis than X. granatum. Overall, our results provided important insights into the variation of genetic structure and adaptation mechanism at interspecific (three Xylocarpus species) and intergeneric (mangrove and non-mangrove genera) levels.

Comparative Chloroplast Genomes of Nicotiana Species (Solanaceae): Insights Into the Genetic Variation, Phylogenetic Relationship, and Polyploid Speciation

Nicotiana L. is a genus rich in polyploidy, which represents an ideal natural system for investigating speciation, biodiversity, and phytogeography. Despite a wealth of phylogenetic work on this genus, a robust evolutionary framework with a dated molecular phylogeny for the genus is still lacking. In this study, the 19 complete chloroplast genomes of Nicotiana species were assembled, and five published chloroplast genomes of Nicotiana were retrieved for comparative analyses. The results showed that the 24 chloroplast genomes of Nicotiana, ranging from 155,327 bp (N. paniculata) to 156,142 bp (N. heterantha) in size, exhibited typical quadripartite structure. The chloroplast genomes were rather conserved in genome structure, GC content, RNA editing sites, and gene content and order. The higher GC content observed in the IR regions could be a result of the presence of abundant rRNA and tRNA genes, which contained a relatively higher GC content. A total of seven hypervariable regions, as new molecular markers for phylogenetic analysis, were uncovered. Based on 78 protein-coding genes, we constructed a well-supported phylogenetic tree, which was largely in agreement with previous studies, except for a slight conflict in several sections. Chloroplast phylogenetic results indicated that the progenitors of diploid N. sylvestris, N. knightiana, and the common ancestor of N. sylvestris and N. glauca might have donated the maternal genomes of allopolyploid N. tabacum, N. rustica, and section Repandae, respectively. Meanwhile, the diploid section Noctiflorae lineages (N. glauca) acted as the most likely maternal progenitor of section Suaveolentes. Molecular dating results show that the polyploid events range considerably in ~0.12 million (section Nicotiana) to ~5.77 million (section Repandae) years ago. The younger polyploids (N. tabacum and N. rustica) were estimated to have arisen ~0.120 and ~0.186 Mya, respectively. The older polyploids (section Repandae and Suaveolentes) were considered to have originated from a single polyploid event at ~5.77 and ~4.49 Mya, respectively. In summary, the comparative analysis of chloroplast genomes of Nicotiana species has not only revealed a series of new insights into the genetic variation and phylogenetic relationships in Nicotiana but also provided rich genetic resources for speciation and biodiversity research in the future.

Comparative Analysis and Phylogenetic Relationships of Ceriops Species (Rhizophoraceae) and Avicennia lanata (Acanthaceae): Insight into the Chloroplast Genome Evolution between Middle and Seaward Zones of Mangrove Forests

Ceriops and Avicennia are true mangroves in the middle and seaward zones of mangrove forests, respectively. The chloroplast genomes of Ceriops decandra, Ceriops zippeliana, and Ceriops tagal were assembled into lengths of 166,650, 166,083 and 164,432 bp, respectively, whereas Avicennia lanata was 148,264 bp in length. The gene content and gene order are highly conserved among these species. The chloroplast genome contains 125 genes in A. lanata and 129 genes in Ceriops species. Three duplicate genes (rpl2, rpl23, and trnM-CAU) were found in the IR regions of the three Ceriops species, resulting in expansion of the IR regions. The rpl32 gene was lost in C. zippeliana, whereas the infA gene was present in A. lanata. Short repeats (<40 bp) and a lower number of SSRs were found in A. lanata but not in Ceriops species. The phylogenetic analysis supports that all Ceriops species are clustered in Rhizophoraceae and A. lanata is in Acanthaceae. In a search for genes under selective pressures of coastal environments, the rps7 gene was under positive selection compared with non-mangrove species. Finally, two specific primer sets were developed for species identification of the three Ceriops species. Thus, this finding provides insightful genetic information for evolutionary relationships and molecular markers in Ceriops and Avicennia species.

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

BACKGROUND

Ziziphus hajarensis is an endemic plant species well-distributed in the Western Hajar mountains of Oman. Despite its potential medicinal uses, little is known regarding its genomic architecture, phylogenetic position, or evolution. Here we sequenced and analyzed the entire chloroplast (cp) genome of Z. hajarensis to understand its genetic organization, structure, and phylogenomic disposition among Rhamnaceae species.

RESULTS

The results revealed the genome of Z. hajarensis cp comprised 162,162 bp and exhibited a typical quadripartite structure, with a large single copy (LSC) region of 895,67 bp, a small single copy (SSC) region of 19,597 bp and an inverted repeat (IR) regions of 26,499 bp. In addition, the cp genome of Z. hajarensis comprises 126 genes, including 82 protein-coding genes, eight rRNA genes, and 36 tRNA genes. Furthermore, the analysis revealed 208 microsatellites, 96.6% of which were mononucleotides. Similarly, a total of 140 repeats were identified, including 11 palindromic, 24 forward, 14 reverse, and 104 tandem repeats. The whole cp genome comparison of Z. hajarensis and nine other species from family Rhamnaceae showed an overall high degree of sequence similarity, with divergence among some intergenic spacers. Comparative phylogenetic analysis based on the complete cp genome, 66 shared genes and matK gene revealed that Z. hajarensis shares a clade with Z. jujuba and that the family Rhamnaceae is the closest family to Barbeyaceae and Elaeagnaceae.

CONCLUSION

All the genome features such as genome size, GC content, genome organization and gene order were highly conserved compared to the other related genomes. The whole cp genome of Z. hajarensis gives fascinating insights and valuable data that may be used to identify related species and reconstruct the phylogeny of the species.

Genetic and molecular mechanisms underlying mangrove adaptations to intertidal environments

Mangroves are halophytic plants belonging to diverse angiosperm families that are adapted to highly stressful intertidal zones between land and sea. They are special, unique, and one of the most productive ecosystems that play enormous ecological roles and provide a large number of benefits to the coastal communities. To thrive under highly stressful conditions, mangroves have innovated several key morphological, anatomical, and physio-biochemical adaptations. The evolution of the unique adaptive modifications might have resulted from a host of genetic and molecular changes and to date we know little about the nature of these genetic and molecular changes. Although slow, new information has accumulated over the last few decades on the genetic and molecular regulation of the mangrove adaptations, a comprehensive review on it is not yet available. This review provides up-to-date consolidated information on the genetic, epigenetic, and molecular regulation of mangrove adaptive traits.

In vitro antifungal and antibacterial potentials of organic extracts of Avicennia marina collected from Rabigh Lagoon, Red Sea Coasts in Saudi Arabia

Abstract Mangrove shrub Avicennia marina (Forsk.) Vierh was used to test the antifungal and antibacterial activities of aerial fractions in vitro. Aspergillus sp, Candida sp and Gram positive bacteria have all been found to be sensitive to mangrove extracts, whereas Gram negative bacteria have been found to be resistant to them. Agar disc diffusion and well-cut diffusion were employed to conduct antifungal and antibacterial activities. The MICs (minimum inhibitory concentrations) for each assay have been established. Several extracts from Mangrove reduced fungus growth (diameters fluctuated between 11 and 41 mm). The Ethyl acetate fraction showed particularly strong inhibition of C. tropicalis, C. albicanis, and A. fumigatus. They had 41, 40, and 25 mm-diameter inhibition zones, respectively. Nesoral, a synthetic antifungal medication, showed no significant changes in its MICs compared to different extracts. Enterococcus faecalis and Bacillus subtilis were inhibited by Petroleum Ether extracts at MICs of 0.78 and 0.35 mg/mL, respectively. It is possible that A. marina extracts may be exploited as a viable natural alternative that may be employed in the management of various infections, notably nosocomial bacterial infections, as anti-candidiasis and as anti-aspergillosis agents.

Comparative study among Avicennia marina, Phragmites australis, and Moringa oleifera based ethanolic-extracts for their antimicrobial, antioxidant, and cytotoxic activities

Microbial resistance and other emerging health risk problems related to the side effects of synthetic drugs are the major factors that result in the research regarding natural products. Fruits, leaves, seeds, and oils-based phyto-constituents are the most important source of pharmaceutical products. Plant extract chemistry depends largely on species, plant components, solvent utilized, and extraction technique. This study was aimed to compare the ethanolic extracts of a mangrove plant, i.e., Avicennia marina (1E: Lower half of A. marina‘s pneumatophores, 2E: A. marina‘s leaves, 3E: Upper half of A. marina‘s pneumatophores, and 4E: A. marina‘s shoots), with non-mangrove plants, i.e., Phragmites australis (5E: P. australis‘s shoot), and Moringa oleifera (6E: M. oleifera‘s leaves) for their antimicrobial activities, total phenolic contents, antioxidant activity, and cytotoxicity potential. The antimicrobial activity assays were performed on gram-positive bacteria (i.e., Bacillus subtilis and Staphylococcus aureus), gram-negative bacteria (i.e., Escherichia coli, and Pseudomonas aeruginosa), and fungi (i.e., Aspergillus niger, Candida albicans, and Rhizopus spp.). We estimated antioxidant activity by TAC, DPPH, and FRAP assays, and the cytotoxicity was evaluated by MTT assay. The results of antimicrobial activities revealed that B. subtilis was the most sensitive to the tested plant extracts compared to S. aureus, while it only showed sensitivity to 6E and Imipenem. 5E and 6E showed statistically similar results against P. aeruginosa as compared to Ceftazidime. E. coli was the most resistant bacteria against tested plant extracts. Among the tested plant extracts, maximum inhibition activity was observed by 6E against A. niger (22 ± 0.57 mm), which was statistically similar to the response of 6E against C. albicans and 3E against Rhizopus spp. 2E did not show any activity against tested fungi. We found that 6E (208.54 ± 1.92 mg g⁻¹) contains maximum phenolic contents followed by 1E (159.42 ± 3.22 mg g⁻¹), 5E (131.08 ± 3.10 mg g⁻¹), 4E (i.e., 72.41 ± 2.96 mg g⁻¹), 3E (67.41 ± 1.68 mg g⁻¹), and 2E (48.72 ± 1.71 mg g⁻¹). The results depict a significant positive correlation between the phenolic contents and the antioxidant activities. As a result, phenolic content may be a natural antioxidant source.