Ancient Geographical Barriers Drive Differentiation among Sonneratia caseolaris Populations and Recent Divergence from S. lanceolata

Genetic diversity and population structure of natural provenances of Sonneratia caseolaris in Vietnam

BACKGROUND

Sommeratia caseolaris is considered the most important mangrove species for reforestation and conservation programs. Therefore, the knowledge of genetic diversity and the population structure of the species has important implications both for the conservation of existing genetic resources and development programs. In the present study, the genetic diversity and structure population of eight populations of S. caseolaris from the Northern to the Southern Coast of Vietnam were determined using nine ISSR molecular markers.

RESULTS

Eight populations of the mangrove species Sonneratia caseolaris were sampled across the natural range in Vietnam to evaluate the genetic diversity of the species. Nine ISSR markers were used to analyse 30 individuals from each population. There were moderate to high levels of genetic diversity (I = 0.447; h = 0.300). PCoA analysis gave very similar results to UPGMA dendrogram construction with the eight populations clustered into three genetic groups which mostly aligned with geographical distances among them. AMOVA analysis results indicated that most (81 %) of the genetic variation was within populations.

CONCLUSION

The current study also indicates the high level of genetic variation existing among and within the natural population of S. caseolaris in Vietnam. These results open new perspectives towards the conservation of the species' genetic resources and their future use in conservation and reforestation programs.

Comparative transcriptome analysis unveiling reactive oxygen species scavenging system of Sonneratia caseolaris under salinity stress

Many mangrove forests have undergone major changes as a result of human activity and global climate change. Sonneratia caseolaris is a common tree located in inner mangroves, and its range extends inland along tidal creeks, as far as the influence of salinity extends. This study investigated the physiological and molecular response mechanisms of S. caseolaris by analyzing its antioxidant defense capacity, including its differentially expressed genes (DEGs) under similar salt stress conditions. Salt treatment significantly affected the osmoprotectants and lipid peroxidation in S. caseolaris seedlings, which increased proline (Pro) content by 31.01-54.90% during all sample periods and decreased malonaldehyde (MDA) content by 12.81 and 18.17% at 25 and 40 days under 3.0% NaCl treatment. Antioxidant enzyme activities increased significantly following 3.0% NaCl treatment. Transcriptome analysis following De novo assembly showed 26,498 matched unigenes. The results showed that 1,263 DEGs responded to transcription factors (TFs) and plant phytohormones and mediated oxidoreductase activity to scavenge reactive oxygen species (ROS) in the control vs. 3.0% NaCl comparison. In addition, the transcription levels of genes associated with auxin and ethylene signal transduction also changed. Under salt stress, ROS scavenging genes (POD, CAT, and APX) and part of AP2, MYB, NAC, C2C2, bHLH, and WRKY TFs were upregulated. This study identified important pathways and candidate genes involved in S. caseolaris salinity tolerance and provided suggestions for further research into the mechanisms of salt tolerance in S. caseolaris.

Mangrove restoration promotes the anti-scouribility of the sediments by modifying inherent microbial community and extracellular polymeric substance

Coastal erosion will aggravate the loss of shorelines and threaten the safety of coastal engineering facilities. Mangrove is often considered as an efficient coastal guard; however the mechanisms involved in anti-scouribility ascribed to mangrove are still poorly understood. Thus, two artificial mangrove forests (including exotic Sonneratia apetala and native Kandelia obovata) and an unvegetated mudflat control were selected to explore the potential function of microbial extracellular polymeric substance (EPS) on the anti-scouribility of the sediments. A cohesive strength meter was used for the analysis of anti-scouribility, while a sequential extraction and 16S high-throughput sequencing were employed to evaluate the changes in EPS and microbial community driven by mangrove restoration. Principal component, redundancy, and two-matrix correlation heatmap analyses were performed for the analyses of the correlations among shear stress, EPS, microbes, and soil properties. The results showed an obvious enhancement of anti-scouribility after mangrove restoration. Compared to those of unvegetated mudflat, shear stress increased from 1.94 N/m² to 3.26 and 4.93 N/m² in the sediments of S. apetala and K. obovata stands, respectively. Mangrove restoration also promoted EPS content in the sediments, irrespective of EPS components and sub-fractions. Both extracellular protein and polysaccharide were found to be positively correlated with anti-scouribility. Coinciding with increased anti-scouribility and EPS, increased bacterial abundances were also detected in the sediments after mangrove restoration (especially K. obovata), whereas Proteobacteria and Bacteroides may be important and influential for EPS secretion and anti-scouribility promotion. Nevertheless, increased total organic carbon, total nitrogen and total phosphorus induced by mangrove restoration may also partially contribute to improvement of anti-scouribility. In conclusion, this is the first study to provide evidence for a link between mangrove restoration and increased EPS which improve resistance to scouring. The present study provides a novel perspective on the revealing of the function of mangrove on erosion mitigation.

Population subdivision promoted by a sea-level-change-driven bottleneck: A glimpse from the evolutionary history of the mangrove plant Aegiceras corniculatum

Historic climate changes drive geographical populations of coastal plants to contract and recover dynamically, even die out completely. Species suffering from such bottlenecks usually lose intraspecific genetic diversity, but how do these events influence population subdivision patterns of coastal plants? Here, we investigated this question in the typical coastal plant: mangrove species Aegiceras corniculatum. Inhabiting the intertidal zone of the tropical and subtropical coast of the Indo-West Pacific oceans, its populations are deemed to be greatly shaped by historic sea-level fluctuations. Using dual methods of Sanger and Illumina sequencing, we found that the 18 sampled populations were structured into two groups, namely, the "Indo-Malayan" group, comprising three subgroups (the northern South China Sea, Gulf of Bengal, and Bali), and the "Pan-Australasia" group, comprising the subgroups of the southern South China Sea and Australasia. Based on the approximate Bayesian computations and Stairway Plot, we inferred that the southern South China Sea subgroup, which penetrates the interior of the "Indo-Malayan" group, originated from the Australasia subgroup, accompanied by a severe bottleneck event, with a spot of gene flow from both the Australasia and "Indo-Malayan" groups. Geographical barriers such as the Sundaland underlie the genetic break between Indian and Pacific Oceans, but the discontinuity between southern and northern South China Sea was originated from genetic drift in the bottleneck event. Hence, we revealed a case evidencing that the bottleneck event promoted population subdivision. This conclusion may be applicable in other taxa beyond coastal plants.

Contrasting Phylogeographic Patterns in Lumnitzera Mangroves Across the Indo-West Pacific

Mangroves are ecologically important forest communities in tropical and subtropical coasts, the effective management of which requires understanding of their phylogeographic patterns. However, these patterns often vary among different species, even among ecologically similar taxa or congeneric species. Here, we investigated the levels and patterns of genetic variation within Lumnitzera consisting of two species (L. racemosa and L. littorea) with nearly sympatric ranges across the Indo-West Pacific (IWP) region by sequencing three chloroplast DNA regions (for both species) and genotyping 11 nuclear microsatellite loci (for L. littorea). Consistent with findings in studies on other mangrove species, we found that both L. racemosa and L. littorea showed relatively high genetic variation among populations but low genetic variation within populations. Haplotype network and genetic clustering analyses indicated two well-differentiated clades in both L. racemosa and L. littorea. The relationship between geographic and genetic distances and divergence time estimates of the haplotypes indicated that limited dispersal ability of the propagules, emergence of land barriers during ancient sea-level changes, and contemporary oceanic circulation pattern in the IWP influenced the current population structure of the two species. However, the position of genetic break was found to vary between the two species: in L. racemosa, strong divergence was observed between populations from the Indian Ocean and the Pacific Ocean possibly due to land barrier effect of the Malay Peninsula; in L. littorea, the phylogeographic pattern was created by a more eastward genetic break along the biogeographic barrier identified as the Huxley's line. Overall, our findings strongly supported previous hypothesis of mangrove species divergence and revealed that the two Lumnitzera species have different phylogeographic patterns despite their close genetic relationship and similar current geographic distribution. The findings also provided references for the management of Lumnitzera mangroves, especially for the threatened L. littorea.

Weak Effect of Gypsy Retrotransposon Bursts on Sonneratia alba Salt Stress Gene Expression

Transposable elements (TEs) are an important source of genetic diversity and can be co-opted for the regulation of host genes. However, to what extent the pervasive TE colonization of plant genomes has contributed to stress adaptation remains controversial. Plants inhabiting harsh environments in nature provide a unique opportunity to answer this question. We compared TE compositions and their evolutionary dynamics in the genomes of two mangrove species: the pioneer Sonneratia alba and its less salt-tolerant relative S. caseolaris. Age distribution, strength of purifying selection and the removal rate of LTR (long terminal repeat) retrotransposons were estimated. Phylogenetic analysis of LTR retrotransposons and their distribution in the genome of S. alba were surveyed. Small RNA sequencing and whole-genome bisulfite sequencing was conducted using leaves of S. alba. Expression pattern of LTR retrotransposons and their nearby genes were examined using RNA-seq data of S. alba under different salt treatments. S. alba possesses more TEs than S. caseolaris. Particularly, many more young Gypsy LTR retrotransposons have accumulated in S. alba than in S. caseolaris despite an increase in purifying selection against TE insertions. The top two most abundant Gypsy families in S. alba preferentially insert in gene-poor regions. They are under relaxed epigenetic repression, probably due to the presence of CHROMO domains in their 3'-ends. Although a considerable number of TEs in S. alba showed differential expression under salt stress, only four copies were significantly correlated with their nearby genes in expression levels. One such TE-gene pair involves Abscisic acid 8'-hydroxylase 3 functioning in abscisic acid catabolism. This study sheds light on the evolutionary dynamics and potential function of TEs in an extremophile. Our results suggest that the conclusion on co-option of TEs should be cautious even though activation of TEs by stress might be prevalent.

Description of a new natural Sonneratia hybrid from Hainan Island, China

Here, we describe, illustrate and compare a new natural hybrid, Sonneratia × zhongcairongii Y. S. Wang & S. H. Shi (Sonneratiaceae), with its possible parent species. Based on its morphological characteristics and habitat conditions, this taxon is considered to represent a sterile hybrid between S. alba and S. apetala. In China, the new hybrid is only reported in the mangrove forest in Dongzhai Harbour, Hainan Island. It has intermediate characteristics with its parents by elliptical leaf blades, peltate stigma, terminal or axillary inflorescence with 1-3 flower dichasia, cup - shaped calyx (4-6 calyx lobes) and no petals. We also provide a key for the identification of Sonneratia species.

Description of a new natural Sonneratia hybrid from Hainan Island, China

Here, we describe, illustrate and compare a new natural hybrid, Sonneratia × zhongcairongii Y. S. Wang & S. H. Shi (Sonneratiaceae), with its possible parent species. Based on its morphological characteristics and habitat conditions, this taxon is considered to represent a sterile hybrid between S. alba and S. apetala. In China, the new hybrid is only reported in the mangrove forest in Dongzhai Harbour, Hainan Island. It has intermediate characteristics with its parents by elliptical leaf blades, peltate stigma, terminal or axillary inflorescence with 1-3 flower dichasia, cup - shaped calyx (4-6 calyx lobes) and no petals. We also provide a key for the identification of Sonneratia species.

Population Differentiation and Demographic History of the Cycas taiwaniana Complex (Cycadaceae) Endemic to South China as Indicated by DNA Sequences and Microsatellite Markers

Historical geology, climatic oscillations, and seed dispersal capabilities are thought to influence the population dynamics and genetics of plants, especially for distribution-restricted and threatened species. Investigating the genetic resources within and among taxa is a prerequisite for conservation management. The Cycas taiwaniana complex consists of six endangered species that are endemic to South China. In this study, we investigated the relationship between phylogeographic history and the genetic structure of the C. taiwaniana complex. To estimate the phylogeographic history of the complex, we assessed the genetic structure and divergence time, and performed phylogenetic and demographic historical analyses. Two chloroplast DNA intergenic regions (cpDNA), two single-copy nuclear genes (SCNGs), and six microsatellite loci (SSR) were sequenced for 18 populations. The SCNG data indicated a high genetic diversity within populations, a low genetic diversity among populations, and significant genetic differentiation among populations. Significant phylogeographical structure was detected. Structure and phylogenetic analyses both revealed that the 18 populations of the C. taiwaniana complex have two main lineages, which were estimated to diverge in the Middle Pleistocene. We propose that Cycas fairylakea was incorporated into Cycas szechuanensis and that the other populations, which are mainly located on Hainan Island, merged into one lineage. Bayesian skyline plot analyses revealed that the C. taiwaniana complex experienced a recent decline, suggesting that the complex probably experienced a bottleneck event. We infer that the genetic structure of the C. taiwaniana complex has been affected by Pleistocene climate shifts, sea-level oscillations, and human activities. In addition to providing new insights into the evolutionary legacy of the genus, the genetic characterizations will be useful for the conservation of Cycas species.