From swamp to field: how genes from mangroves and its associates can enhance crop salinity tolerance.

Salinity stress is a critical challenge in crop production and requires innovative strategies to enhance the salt tolerance of plants. Insights from mangrove species, which are renowned for their adaptability to high-salinity environments, provides valuable genetic targets and resources for improving crops. A significant hurdle in salinity stress is the excessive uptake of sodium ions (Na+) by plant roots, causing disruptions in cellular balance, nutrient deficiencies, and hampered growth. Specific ion transporters and channels play crucial roles in maintaining a low Na+/K+ ratio in root cells which is pivotal for salt tolerance. The family of high-affinity potassium transporters, recently characterized in Avicennia officinalis, contributes to K+ homeostasis in transgenic Arabidopsis plants even under high-salt conditions. The salt overly sensitive pathway and genes related to vacuolar-type H+-ATPases hold promise for expelling cytosolic Na+ and sequestering Na+ in transgenic plants, respectively. Aquaporins contribute to mangroves' adaptation to saline environments by regulating water uptake, transpiration, and osmotic balance. Antioxidant enzymes mitigate oxidative damage, whereas genes regulating osmolytes, such as glycine betaine and proline, provide osmoprotection. Mangroves exhibit increased expression of stress-responsive transcription factors such as MYB, NAC, and CBFs under high salinity. Moreover, genes involved in various metabolic pathways, including jasmonate synthesis, triterpenoid production, and protein stability under salt stress, have been identified. This review highlights the potential of mangrove genes to enhance salt tolerance of crops. Further research is imperative to fully comprehend and apply these genes to crop breeding to improve salinity resilience.

Rapid diversification of grey mangroves (Avicennia marina) driven by geographic isolation and extreme environmental conditions in the Arabian Peninsula.

Biological systems occurring in ecologically heterogeneous and spatially discontinuous habitats provide an ideal opportunity to investigate the relative roles of neutral and selective factors in driving lineage diversification. The grey mangroves (Avicennia marina) of Arabia occur at the northern edge of the species' range and are subject to variable, often extreme, environmental conditions, as well as historic large fluctuations in habitat availability and connectivity resulting from Quaternary glacial cycles. Here, we analyse fully sequenced genomes sampled from 19 locations across the Red Sea, the Arabian Sea and the Persian/Arabian Gulf (PAG) to reconstruct the evolutionary history of the species in the region and to identify adaptive mechanisms of lineage diversification. Population structure and phylogenetic analyses revealed marked genetic structure correlating with geographic distance and highly supported clades among and within the seas surrounding the Arabian Peninsula. Demographic modelling showed times of divergence consistent with recent periods of geographic isolation and low marine connectivity during glaciations, suggesting the presence of (cryptic) glacial refugia in the Red Sea and the PAG. Significant migration was detected within the Red Sea and the PAG, and across the Strait of Hormuz to the Arabian Sea, suggesting gene flow upon secondary contact among populations. Genetic-environment association analyses revealed high levels of adaptive divergence and detected signs of multi-loci local adaptation driven by temperature extremes and hypersalinity. These results support a process of rapid diversification resulting from the combined effects of historical factors and ecological selection and reveal mangrove peripheral environments as relevant drivers of lineage diversity.

Functional characterization of a manganese superoxide dismutase from Avicennia marina: insights into its role in salt, hydrogen peroxide, and heavy metal tolerance.

Avicennia marina is a salt-tolerance plant with high antioxidant and antibacterial potential. In the present work, a gene encoding MnSOD from Avicennia marina (AmSOD2) was cloned in the expression vectors pET28a. The resulting constructs were transformed into Escherichia coli strains Rosetta (DE3). Following the induction with Isopropyl ß-D-1-thiogalactopyranoside, the protein His-AmSOD2 was expressed but dominantly found in the insoluble fraction of strain R-AmSOD2. Due to detection of mitochondrial transit peptide in the amino acid sequence of AmSOD2, the transit peptide was removed and AmSOD2 without transit peptide (tAmSOD2) was expressed in E. coli and dominantly found in the soluble fraction. The enzyme His-tAmSOD2 exhibited a molecular mass of 116 kDa in native condition. Nevertheless, in reducing conditions the molecular mass is 28 kDa indicating the enzyme His-tAmSOD2 is a tetramer protein. As shown by ICP analysis there is one mole Mn2+ in each monomer. The Pure His-tAmSOD2 was highly active in vitro, however the activity was almost three-fold lower than His-AmSOD1. Whereas the high stability of the recombinant His-AmSOD1was previously shown after incubation in a broad range pH and high temperature, His-tAmSOD2 was stable up to 50 °C and pH 6 for 1 h. The gene expression analysis showed that the gene encoding AmSOD2 is expressed in root, shoot and leaves of A. marina. In addition, the results show that the expression in the leaves was enhanced after treatment of plant with NaCl, H2O2, Cd2+ and Ni2+ indicating the important role of MnSOD in the resistant mechanism of mangroves.

Comparative Transcriptomics and Metabolomics Analyses of Avicennia marina and Kandelia obovata under Chilling Stress during Seedling Stage.

One of the most productive ecosystems in the world, mangroves are susceptible to cold stress. However, there is currently insufficient knowledge of the adaptation mechanisms of mangrove plants in response to chilling stress. This study conducted a comparative analysis of transcriptomics and metabolomics to investigate the adaptive responses of Kandelia obovata (chilling-tolerant) and Avicennia marina (chilling-sensitive) to 5 °C. The transcriptomics results revealed that differentially expressed genes (DEGs) were mostly enriched in signal transduction, photosynthesis-related pathways, and phenylpropanoid biosynthesis. The expression pattern of genes involved in photosynthesis-related pathways in A. marina presented a downregulation of most DEGs, which correlated with the decrease in total chlorophyll content. In the susceptible A. marina, all DEGs encoding mitogen-activated protein kinase were upregulated. Phenylpropanoid-related genes were observed to be highly induced in K. obovata. Additionally, several metabolites, such as 4-aminobutyric acid, exhibited higher levels in K. obovata than in A. marina, suggesting that chilling-tolerant varieties regulated more metabolites in response to chilling. The investigation defined the inherent distinctions between K. obovata and A. marina in terms of signal transduction gene expression, as well as phenylpropanoid and flavonoid biosynthesis, during exposure to low temperatures.

Combined metabolome and transcriptome analysis reveals a critical role of lignin biosynthesis and lignification in stem-like pneumatophore development of the mangrove Avicennia marina.

MAIN CONCLUSION: Transcriptional and metabolic regulation of lignin biosynthesis and lignification plays crucial roles in Avicennia marina pneumatophore development, facilitating its adaptation to coastal habitats. Avicennia marina is a pioneer mangrove species in coastal wetland. To cope with the periodic intertidal flooding and hypoxia environment, this species has developed a complex and extensive root system, with its most unique feature being a pneumatophore with a distinct above- and below-ground morphology and vascular structure. However, the characteristics of pneumatophore lignification remain unknown. Studies comparing the anatomy among above-ground pneumatophore, below-ground pneumatophore, and feeding root have suggested that vascular structure development in the pneumatophore is more like the development of a stem than of a root. Metabolome and transcriptome analysis illustrated that the accumulation of syringyl (S) and guaiacyl (G) units in the pneumatophore plays a critical role in lignification of the stem-like structure. Fourteen differentially accumulated metabolites (DAMs) and 10 differentially expressed genes involved in the lignin biosynthesis pathway were targeted. To identify genes significantly associated with lignification, we analyzed the correlation between 14 genes and 8 metabolites and further built a co-expression network between 10 transcription factors (TFs), including 5 for each of MYB and NAC, and 23 enzyme-coding genes involved in lignin biosynthesis. 4-Coumarate-CoA ligase, shikimate/quinate hydroxycinnamoyl transferase, cinnamyl alcohol dehydrogenase, caffeic acid 3-O-methyltransferase, phenylalanine ammonia-lyase, and peroxidase were identified to be strongly correlated with these TFs. Finally, we examined 9 key candidate genes through quantitative real-time PCR to validate the reliability of transcriptome data. Together, our metabolome and transcriptome findings reveal that lignin biosynthesis and lignification regulate pneumatophore development in the mangrove species A. marina and facilitate its adaptation to coastal habitats.

Studies on genetic diversity, gene flow and landscape genetic in Avicennia marina: Spatial PCA, Random Forest, and phylogeography approaches.

Mangrove forests grow in coastal areas, lagoons, estuaries, and deltas and form the main vegetation in tidal and saline wetlands. Due to the mankind activities and also changes in climate, these forests face degradations and probably extinction in some areas. Avicennia marina is one of the most distributed mangrove species throughout the world. The populations of A. marina occur in a limited region in southern parts of Iran. Very few genetic and spatial analyses are available on these plants from our country. Therefore, the present study was planned to provide detailed information on Avicennia marina populations with regard to genetic diversity, gene flow versus genetic isolation, effects of spatial variables on connectivity and structuring the genetic content of trees populations and also identifying adaptive genetic regions in respond too spatial variables. We used SCoT molecular markers for genetic analyses and utilized different computational approaches for population genetics and landscapes analyses. The results of present study showed a low to moderate genetic diversity in the studied populations and presence of significant Fst values among them. Genetic fragmentation was also observed within each province studied. A limited gene flow was noticed among neighboring populations within a particular province. One population was almost completely isolated from the gene flow with other populations and had peculiar genetic content.Spatial PCA analysis revealed both significant global and local genetic structuring in the studied populations. Spatial variables like humidity, longitude and altitude were the most important spatial features affecting genetic structure in these populations.

Inventory of cadmium-transporter genes in the root of mangrove plant Avicennia marina under cadmium stress.

Mangrove Avicennia marina has the importantly potential for cadmium (Cd) pollution remediation in coastal wetlands. Unfortunately, the molecular mechanisms and transporter members for Cd uptake by the roots of A. marina are not well documented. In this study, photosynthetic and phenotypic analysis indicated that A. marina is particularly tolerant to Cd. The content and flux analysis indicated that Cd is mainly retained in the roots, with greater Cd influx in fine roots than that in coarse roots, and higher Cd influx in the root meristem zone as well. Using transcriptomic analysis, a total of 5238 differentially expressed genes were identified between the Cd treatment and control group. Moreover, we found that 54 genes were responsible for inorganic ion transport. Among these genes, AmHMA2, AmIRT1, and AmPCR2 were localized in the plasma membrane and AmZIP1 was localized in both plasma membrane and cytoplasm. All above gene encoding transporters showed significant Cd transport activities using function assay in yeast cells. In addition, the overexpression of AmZIP1 or AmPCR2 in Arabidopsis improved the Cd tolerance of transgenic plants. This is particularly significant as it provides insight into the molecular mechanism for Cd uptake by the roots of mangrove plants and a theoretical basis for coastal wetland phytoremediation.

Complete genome sequence analysis of plant growth-promoting bacterium, Isoptericola sp. AK164 isolated from the rhizosphere of Avicennia marina growing at the Red Sea coast.

Isoptericola sp. AK164 is a Gram-positive, aerobic bacterial genus from the family Promicromonosporaceae, isolated from the root rhizosphere of Avicennia marina. AK164 significantly enhanced the growth of the Arabidopsis thaliana plant under normal and saline conditions. These bacteria can produce ACC deaminase and several enzymes playing a role in carbohydrate hydrolyses, such as cellulose, hemicellulose, and chitin degradation, which may contribute to plant growth, salt tolerance, and stress elevation. The genome sequence AK164 has a single circular chromosome of approximately 3.57 Mbp with a GC content of 73.53%. A whole genome sequence comparison of AK164 with type strains from the same genus, using digital DNA-DNA hybridization and average nucleotide identity calculations, revealed that AK164 might potentially belong to a new species of Isoptericola. Genome data and biochemical analyses indicate that AK164 could be a potential biostimulant for improving agriculture in submerged saline land.

Putative Local Adaptive SNPs in the Genus Avicennia.

The genus Avicennia with eight species grow in intertidal zones of tropical and temperate regions, ranging in distribution from West Asia, to Australia, and Latin America. These mangroves have several medicinal applications for mankind. Many genetic and phylogenetic studies have been carried out on mangroves, but none is concerned with geographical adaptation of SNPs. We therefore, used ITS sequences of about 120 Avicennia taxa growing in different parts of the world and undertook computational analyses to identify discriminating SNPs among these species and to study their association with geographical variables. A combination of multivariate and Bayesian approaches such as CCA, RDA, and LFMM were conducted to identify the SNPs with potential adaptation to geographical and ecological variables. Manhattan plot revealed that many of these SNPs are significantly associated with these variables. The genetic changes accompanied by local and geographical adaptation were illustrated by skyline plot. These genetic changes occurred not under a molecular clock model of evolution and probably under a positive selection pressure imposed in different geographical regions in which these plants grow.

Genome wide identification and characterization of MATE family genes in mangrove plants.

Multidrug and Toxic Compound Extrusion (MATE) proteins are essential transporters that extrude metabolites and participate in plant development and cellular detoxification. MATE transporters, which play crucial roles in the survival of mangrove plants under highly challenged environments, by specialized salt extrusion mechanisms, are mined from their genomes and reported here for the first time. Through homology search and domain prediction in the genome assemblies of Avicennia marina, Bruguiera sexangula, Ceriops zippeliana, Kandelia obovata, Rhizophora apiculata and Ceriops tagal, 74, 68, 66, 66, 63 and 64 MATE proteins, respectively were identified. The phylogenetic analysis divided the identified proteins into five major clusters and following the clustering pattern of the functionally characterized proteins, functions of the transporters in each cluster were predicted. Amino acid sequences, exon-intron structure, motif details and subcellular localization pattern for all the 401 proteins are described. The custom designed repeat masking libraries generated for each of these genomes, which will be of extensive use for the researchers worldwide, are also provided in this paper. This is the first study on the MATE genes in mangroves and the results provide comprehensive information on the molecular mechanisms enabling the survival of mangroves under hostile conditions.

Sediment microbial community structure associated to different ecological types of mangroves in Celestún, a coastal lagoon in the Yucatan Peninsula, Mexico.

Mangroves are unique coastal ecosystems, which have many important ecological functions, as they are a reservoir of many marine species well adapted to saline conditions and are fundamental as sites of carbon storage. Although the microbial contribution to nutrient cycling in these ecosystems has been well recognized, there is a lack of information regarding the microbial composition and structure of different ecological types of mangrove forests. In this study, we characterized the microbial community (Bacteria and Archaea) in sediments associated with five ecological types of mangrove forests in a coastal lagoon dominated by Avicennia germinans and Rhizophora mangle, through 16S rRNA-V4 gene sequencing. Overall, Proteobacteria (51%), Chloroflexi (12%), Gemmatimonadetes (5%) and Planctomycetes (6%) were the most abundant bacterial phyla, while Thaumarchaeota (30%), Bathyarchaeota (21%) and Nanoarchaeaeota (18%) were the dominant archaeal phyla. The microbial composition associated with basin mangroves dominated by Avicennia germinans was significantly different from the other ecological types, which becomes relevant for restoration strategies.

In silico analysis of NAC gene family in the mangrove plant Avicennia marina provides clues for adaptation to intertidal habitats.

NAC (NAM, ATAF1/2, CUC2) transcription factors (TFs) constitute a plant-specific gene family. It is reported that NAC TFs play important roles in plant growth and developmental processes and in response to biotic/abiotic stresses. Nevertheless, little information is known about the functional and evolutionary characteristics of NAC TFs in mangrove plants, a group of species adapting coastal intertidal habitats. Thus, we conducted a comprehensive investigation for NAC TFs in Avicennia marina, one pioneer species of mangrove plants. We totally identified 142 NAC TFs from the genome of A. marina. Combined with NAC proteins having been functionally characterized in other organisms, we built a phylogenetic tree to infer the function of NAC TFs in A. marina. Gene structure and motif sequence analyses suggest the sequence conservation and transcription regulatory regions-mediated functional diversity. Whole-genome duplication serves as the driver force to the evolution of NAC gene family. Moreover, two pairs of NAC genes were identified as positively selected genes of which AmNAC010/040 may be imposed on less constraint toward neofunctionalization. Quite a few stress/hormone-related responsive elements were found in promoter regions indicating potential response to various external factors. Transcriptome data revealed some NAC TFs were involved in pneumatophore and leaf salt gland development and response to salt, flooding and Cd stresses. Gene co-expression analysis found a few NAC TFs participates in the special biological processes concerned with adaptation to intertidal environment. In summary, this study provides detailed functional and evolutionary information about NAC gene family in mangrove plant A. marina and new perspective for adaptation to intertidal habitats.

Jiella avicenniae sp. nov., a novel endophytic bacterium isolated from bark of Avicennia marina.

A Gram-stain-negative and short rod-shaped strain CBK1P-4T, isolated from surface-sterilized bark of Avicennia marina was investigated by a polyphasic taxonomic approach to resolve its taxonomic position. Strain CBK1P-4T grew at 10-30 °C (optimum, 25 °C), pH 5.0-9.0 (optimum, pH 5.5) and in the presence of 0-9% (w/v) NaCl (optimum, 1-2%). Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CBK1P-4T belonged to the genus Jiella and was most closely related to species of the genus Jiella (97.4-98.3%). The genome comparisons between strain CBK1P-4T and the closely related species indicated that average nucleotide identity and digital DNA-DNA hybridization values were below the recommended thresholds for assigning strains to the same species (95-96% and 70%, respectively). The cell wall peptidoglycan contained meso-diaminopimelic acid as diagnostic diamino acid. The principal fatty acids were C18:1ω7c and C19:0cycloω8c. The polar lipids were mainly comprised of phosphatidylcholine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, two unidentified aminolipids, one unidentified phospholipid and one unidentified glycolipid. The dominant respiratory quinone was ubiquinone-10. The DNA G + C content of strain CBK1P-4T was 66.7%. Based on the phenotypic features, phylogenetic analysis as well as genome analysis, we conclude that strain CBK1P-4T represents a novel Jiella species, for which the name Jiella avicenniae sp. nov. is proposed. The type strain is CBK1P-4T (= CGMCC 1.18742T = JCM 34330T).

Metagenomic and genomic characterization of heavy metal tolerance and resistance genes in the rhizosphere microbiome of Avicennia germinans in a semi-arid mangrove forest in the tropics.

Mangroves are often exposed to heavy metals that accumulate in the food chain, generate toxicity to mangrove plants and affect microbial diversity. This study determined the abundance of genes associated with resistance and tolerance to heavy metals in the rhizosphere microbiome of Avicennia germinans from a semi-arid mangrove of La Guajira-Colombia by metagenomics and genomics approach. Twenty-eight genes associated with tolerance and 49 genes related to resistance to heavy metals were detected. Genes associated with tolerance and resistance to Cu, especially cusA and copA, were the most abundant. The highest number of genes for tolerance and resistance were for Zn and Co, respectively. The isolate Vibrio fluvialis showed the ability to tolerate Cu, Ni, Zn, and Cd. This work used a complementary approach of metagenomics and genomics to characterize the potential of mangrove microorganisms to tolerate and resist heavy metals and the influence of salinity on their abundance.

The genome of a mangrove plant, Avicennia marina, provides insights into adaptation to coastal intertidal habitats.

MAIN CONCLUSION: Whole-genome duplication, gene family and lineage-specific genes analysis based on high-quality genome reveal the adaptation mechanisms of Avicennia marina to coastal intertidal habitats. Mangrove plants grow in a complex habitat of coastal intertidal zones with high salinity, hypoxia, etc. Therefore, it is an interesting question how mangroves adapt to the unique intertidal environment. Here, we present a chromosome-level genome of the Avicennia marina, a typical true mangrove with a size of 480.43 Mb, contig N50 of 11.33 Mb and 30,956 annotated protein-coding genes. We identified 621 Avicennia-specific genes that are mainly related to flavonoid and lignin biosynthesis, auxin homeostasis and response to abiotic stimulus. We found that A. marina underwent a novel specific whole-genome duplication, which is in line with a brief era of global warming that occurred during the paleocene-eocene maximum. Comparative genomic and transcriptomic analyses outline the distinct evolution and sophisticated regulations of A. marina adaptation to the intertidal environments, including expansion of photosynthesis and oxidative phosphorylation gene families, unique genes and pathways for antibacterial, detoxifying antioxidant and reactive oxygen species scavenging. In addition, we also analyzed salt gland secretion-related genes, and those involved in the red bark-related flavonoid biosynthesis, while significant expansions of key genes such as NHX, 4CL, CHS and CHI. High-quality genomes in future investigations will facilitate the understand of evolution of mangrove and improve breeding.

Comprehensive characterization and molecular insights into the salt tolerance of a Cu, Zn-superoxide dismutase from an Indian Mangrove, Avicennia marina.

Superoxide dismutases are important group of antioxidant metallozyme and play important role in ROS homeostasis in salinity stress. The present study reports the biochemical properties of a salt-tolerant Cu, Zn-superoxide from Avicennia marina (Am_SOD). Am_SOD was purified from the leaf and identified by mass-spectrometry. Recombinant Am_SOD cDNA was bacterially expressed as a homodimeric protein. Enzyme kinetics revealed a high substrate affinity and specific activity of Am_SOD as compared to many earlier reported SODs. An electronic transition in 360-400 nm spectra of Am_SOD is indicative of Cu2+-binding. Am_SOD activity was potentially inhibited by diethyldithiocarbamate and H2O2, a characteristic of Cu, Zn-SOD. Am_SOD exhibited conformational and functional stability at high NaCl concentration as well in alkaline pH. Introgression of Am_SOD in E. coli conferred tolerance to oxidative stress under highly saline condition. Am_SOD was moderately thermostable and retained functional activity at ~ 60 °C. In-silico analyses revealed 5 solvent-accessible N-terminal residues of Am_SOD that were less hydrophobic than those at similar positions of non-halophilic SODs. Substituting these 5 residues with non-halophilic counterparts resulted in > 50% reduction in salt-tolerance of Am_SOD. This indicates a cumulative role of these residues in maintaining low surface hydrophobicity of Am_SOD and consequently high salt tolerance. The molecular information on antioxidant activity and salt-tolerance of Am_SOD may have potential application in biotechnology research. To our knowledge, this is the first report on salt-tolerant SOD from mangrove.

Evidence for the genetic similarity rule at an expanding mangrove range limit.

PREMISE: Host-plant genetic variation can shape associated communities of organisms. These community-genetic effects include (1) genetically similar hosts harboring similar associated communities (i.e., the genetic similarity rule) and (2) host-plant heterozygosity increasing associated community diversity. Community-genetic effects are predicted to be less prominent in plant systems with limited genetic variation, such as those at distributional range limits. Yet, empirical evidence from such systems is limited. METHODS: We sampled a natural population of a mangrove foundation species (Avicennia germinans) at an expanding range limit in Florida, USA. We measured genetic variation within and among 40 host trees with 24 nuclear microsatellite loci and characterized their foliar endophytic fungal communities with internal transcribed spacer (ITS1) gene amplicon sequencing. We evaluated relationships among host-tree genetic variation, host-tree spatial location, and the associated fungal communities. RESULTS: Genetic diversity was low across all host trees (mean: 2.6 alleles per locus) and associated fungal communities were relatively homogeneous (five sequence variants represented 78% of all reads). We found (1) genetically similar host trees harbored similar fungal communities, with no detectable effect of interhost geographic distance. (2) Host-tree heterozygosity had no detectable effect, while host-tree absolute spatial location affected community alpha diversity. CONCLUSIONS: This research supports the genetic similarity rule within a range limit population and helps broaden the current scope of community genetics theory by demonstrating that community-genetic effects can occur even at expanding distributional limits where host-plant genetic variation may be limited. Our findings also provide the first documentation of community-genetic effects in a natural mangrove system.

A reference-grade genome identifies salt-tolerance genes from the salt-secreting mangrove species Avicennia marina.

Water scarcity and salinity are major challenges facing agriculture today, which can be addressed by engineering plants to grow in the boundless seawater. Understanding the mangrove plants at the molecular level will be necessary for developing such highly salt-tolerant agricultural crops. With this objective, we sequenced the genome of a salt-secreting and extraordinarily salt-tolerant mangrove species, Avicennia marina, that grows optimally in 75% seawater and tolerates >250% seawater. Our reference-grade ~457 Mb genome contains 31 scaffolds corresponding to its chromosomes. We identified 31,477 protein-coding genes and a salinome consisting of 3246 salinity-responsive genes and homologs of 614 experimentally validated salinity tolerance genes. The salinome provides a strong foundation to understand the molecular mechanisms of salinity tolerance in plants and breeding crops suitable for seawater farming.

A high-quality genome assembly and annotation of the gray mangrove, Avicennia marina.

The gray mangrove [Avicennia marina (Forsk.) Vierh.] is the most widely distributed mangrove species, ranging throughout the Indo-West Pacific. It presents remarkable levels of geographic variation both in phenotypic traits and habitat, often occupying extreme environments at the edges of its distribution. However, subspecific evolutionary relationships and adaptive mechanisms remain understudied, especially across populations of the West Indian Ocean. High-quality genomic resources accounting for such variability are also sparse. Here we report the first chromosome-level assembly of the genome of A. marina. We used a previously release draft assembly and proximity ligation libraries Chicago and Dovetail HiC for scaffolding, producing a 456,526,188-bp long genome. The largest 32 scaffolds (22.4-10.5 Mb) accounted for 98% of the genome assembly, with the remaining 2% distributed among much shorter 3,759 scaffolds (62.4-1 kb). We annotated 45,032 protein-coding genes using tissue-specific RNA-seq data in combination with de novo gene prediction, from which 34,442 were associated to GO terms. Genome assembly and annotated set of genes yield a 96.7% and 95.1% completeness score, respectively, when compared with the eudicots BUSCO dataset. Furthermore, an FST survey based on resequencing data successfully identified a set of candidate genes potentially involved in local adaptation and revealed patterns of adaptive variability correlating with a temperature gradient in Arabian mangrove populations. Our A. marina genomic assembly provides a highly valuable resource for genome evolution analysis, as well as for identifying functional genes involved in adaptive processes and speciation.

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

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.