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[Objective] The influence of land use changes on carbon storage were studied under the expansion of urbanization in Hainan Island to reveal the spatial-temporal evolution pattern of carbon storage and to predict future development trends in order to provide scientific evidence for optimizing the spatial layout of the national territory and for protecting ecologically sensitive areas. [Methods] Based on land use data from 1980 to 2020, this research showed the spatial-temporal changes of carbon storage for Hannan Island. The data were used with the carbon storage module of the InVEST model. The FLUS model and the InVEST model were coupled to simulate land use and carbon storage changes for Hainan Island in 2030 under three scenarios: the natural development scenario, the rapid development scenario, and the ecological protection scenario. [Results] ① The main types of land use on Hainan Island were forest land and cultivated land. From 1980 to 2020, the areas of cultivated land, grassland, forest land, and unused land decreased to varying degrees. The area of construction land and water increased over that time period, with the fastest growth rate being 83.4% for construction land. ② Carbon storage for Hainan Island was generally characterized as “higher in the middle and lower in the surrounding areas”. Carbon storage changed slightly from 1980 to 2000, with a decrease of about 0.03%. From 2000 to 2020, the urbanization process on Hainan Island accelerated, and the loss of carbon storage also increased. The average annual loss was about 372 t, and the cumulative loss of carbon storage was 7 439 t. ③ The prediction results showed that construction land will continue to expand in the future, and carbon storage on Hainan Island in 2030 will decrease under the three scenarios. Under the rapid development scenario, the land use change of construction land was the largest, and carbon storage was the most vulnerable to loss, followed by the natural development scenario. The ecological protection scenario had the smallest change. [Conclusion] Land Use Planning for Hainan Free Trade Port in the future should focus on the protecting key ecological areas such as the central mountainous areas, strengthening the nature reserves of Hainan Island, optimizing the land use pattern, and strictly controlling the transformation of forest land, cultivated land, and wetlands into construction land. The efficiency of carbon sequestration should be improved, and forest carbon sinks should be increased to achieve regional sustainable development.

Nypa fruticans, commonly known as the Nipa palm, belongs to the true mangrove plants of the Arecaceae family. In China, it is naturally distributed only on Hainan Island and designated as a second-class National Key Protected Wild Plants List. Field research and indoor simulation experiments were systematically employed to study the resource status of N. fruticans and the adaptation of seed germination to environmental factors. The results showed that: (1) Four natural populations of N. fruticans, approximately 9319 trees within a total area of 3.96 hm2, were distributed in Haikou, Wenchang, Qionghai, and Wanning on Hainan Island. Only the Wanning population was developed in small patches, while other populations were scattered sporadically. (2) A total of 23 mangrove species belonged to 19 genera in 13 families, which were recorded in all study sites, of which 18 were true mangroves and 5 were semi-mangrove species. The vertical structures of 4 N. fruticans communities exhibited the consistent pattern, characterized by distinct layers including the tree, shrub, and herb layers. However, notable differences in species composition and dominant species were observed among the layers of each community. (3) The population dynamics of N. fruticans in Haikou, Qionghai, and Wanning were declining, while the population in Wenchang was growing. (4) Seed germination of N. fruticans was not resistant to strong light and required some shade treatment with an optimal light intensity of 60%. The suitable salinity range for seed germination was 0‰ to 10‰. With the increase of salinity, the germination rate and seedling rate showed an increasing and then decreasing trend with maximum values of 63.3% and 50.0% at 5‰, which showed the sensitivity of seed germination to salinity, with low salinity promoting germination whereas high salinity inhibiting germination. Around 8 h/d of flooding time was most suitable for the seed germination, and 10 h/d was a critical flooding time. This study provides a theoretical basis for population recovery, resource utilization, and other further research of N. fruticans. [ABSTRACT FROM AUTHOR]

In China, Dolichandrone spathacea is a rare and endangered semi-mangrove plant species with an extremely small population, naturally distributed only in Zhanjiang City and the east coast of Hainan Island. Despite conservation concerns, the population status of D. spathacea has received little scientific attention. In this study, we evaluated the current status of D. spathacea on Hainan Island, China, in order to propose sustainable conservation strategies for future ecological restoration of its natural population. D. spathacea on Hainan Island can be divided into four populations. All the D. spathacea populations present a state of overall dispersion, local concentration, and occasionally sporadic existence, and they exist in geographical isolation. The young, middle, and old D. spathacea plants account for 20.42%, 66.20%, and 13.38%, respectively, indicating that the D. spathacea population on Hainan Island is declining. Furthermore, instead of temporal structure, we used diameter at breast height (DBH) to establish a static life table, draw a population survival curve, and quantify the future development trend through population dynamic analysis and time-series prediction. These results suggest that the D. spathacea population in the Bamen Gulf (Wenchang) and Qingmei Harbor (Sanya) on Hainan Island is sensitive to external disturbances and possesses two main increases in mortality rate—namely, in its juvenile and mature stages—due to competition and anthropogenic interferences, which might be the most important reasons for its endangered status. Depending on the current conditions of the D. spathacea population, we should conserve and expand mature trees in situ, preserve their germplasm resources, rehabilitate their habitats to promote provenance restoration, and conduct artificial cultivation and spreading planting in order to realize the sustainable conservation and management of D. spathacea. [ABSTRACT FROM AUTHOR]

Nypa fruticans (Wurmb), a mangrove palm species with origins dating back to the Late Cretaceous period, is a unique species for investigating long‐term adaptation strategies to intertidal environments and the early evolution of palms. Here, we present a chromosome‐level genome sequence and assembly for N. fruticans. We integrated the genomes of N. fruticans and other palm family members for a comparative genomic analysis, which confirmed that the common ancestor of all palms experienced a whole‐genome duplication event around 89 million years ago, shaping the distinctive characteristics observed in this clade. We also inferred a low mutation rate for the N. fruticans genome, which underwent strong purifying selection and evolved slowly, thus contributing to its stability over a long evolutionary period. Moreover, ancient duplicates were preferentially retained, with critical genes having experienced positive selection, enhancing waterlogging tolerance in N. fruticans. Furthermore, we discovered that the pseudogenization of Early Methionine‐labelled 1 (EM1) and EM6 in N. fruticans underly its crypto‐vivipary characteristics, reflecting its intertidal adaptation. Our study provides valuable genomic insights into the evolutionary history, genome stability, and adaptive evolution of the mangrove palm. Our results also shed light on the long‐term adaptation of this species and contribute to our understanding of the evolutionary dynamics in the palm family. [ABSTRACT FROM AUTHOR]

Although gene loss is common in evolution, it remains unclear whether it is an adaptive process. In a survey of seven major mangrove clades that are woody plants in the intertidal zones of daily environmental perturbations, we noticed that they generally evolved reduced gene numbers. We then focused on the largest clade of Rhizophoreae and observed the continual gene set reduction in each of the eight species. A great majority of gene losses are concentrated on environmental interaction processes, presumably to cope with the constant fluctuations in the tidal environments. Genes of the general processes for woody plants are largely retained. In particular, fewer gene losses are found in physiological traits such as viviparous seeds, high salinity, and high tannin content. Given the broad and continual genome reductions, we propose the May–Wigner theory (MWT) of system stability as a possible mechanism. In MWT, the most effective solution for buffering continual perturbations is to reduce the size of the system (or to weaken the total genic interactions). Mangroves are unique as immovable inhabitants of the compound environments in the land–sea interface, where environmental gradients (such as salinity) fluctuate constantly, often drastically. Extending MWT to gene regulatory network (GRN), computer simulations and transcriptome analyses support the stabilizing effects of smaller gene sets in mangroves vis-à-vis inland plants. In summary, we show the adaptive significance of gene losses in mangrove plants, including the specific role of promoting phenotype innovation and a general role in stabilizing GRN in unstable environments as predicted by MWT. [ABSTRACT FROM AUTHOR]

Insect diversity is an indicator of environmental conditions. Frequent outbreaks of mangrove pests have threatened the fragile mangrove ecosystem in China and the sustainable utilization of mangrove resources. The understanding of mangrove pests, as well as a fundamental knowledge of insect diversity, in mangrove forests in China has been hindered by the difficulty of morphological species delimitation because captured insect specimens are either larvae or incompletely preserved adults. DNA barcoding technology uses only a small amount of DNA to conduct species identification. Taking advantage of this, we investigated the entomofauna of mangrove forests on Hainan Island by using a barcode combining cytochrome c oxidase subunit I (COI) and cytochrome-b (Cytb). We collected 627 specimens at six localities around the island, which were identified as 219 insect species belonging to 11 orders and 72 families. Lepidoptera, Coleoptera, and Hymenoptera are the most species-rich and abundant taxa. We also identified 13 mangrove pests, 5 parasitoids, and 12 species of predators.Keywords: DNA barcoding, Hainan Island, mangrove, insect, pest.La diversite des insectes est un indicateur des conditions environnementales. De frequentes eclosions de ravageurs de la mangrove ont menace cet ecosysteme fragile en Chine de meme que l'utilisation durable des ressources de la mangrove. Les difficultes a delimiter les especes sur une base morphologique, soit parce que les specimens captures sont des larves ou des adultes incompletement preserves, ont limite la comprehension des ravageurs et des connaissances fondamentales sur la diversite des insectes dans les forets de mangrove en Chine. La technologie de codage a barres de l'ADN utilise une faible quantite d'ADN pour identifier les especes. Tirant profit de cela, les auteurs ont etudie l'entomofaune des forets de mangrove de l'ile de Hainan au moyen d'un code a barre combinant la sous-unite I de la cytochrome c oxydase (COI) et le cytochrome b (Cytb). Les auteurs ont preleve 627 specimens dans six sites sur l'ile. Ces echantillons ont ete identifies comme etant membres de 219 especes d'insectes appartenant a 11 ordres et 72 familles. Les lepidopteres, les coleopteres et les hymenopteres etaient les taxons les plus riches en especes et les plus abondants. Les auteurs ont egalement identifie 13 ravageurs de la mangrove, 5 parasitoses et 12 especes de predateurs. [Traduit par la Redaction]Mots-cles: codage a barres de l'ADN, ile de Hainan, mangrove, insecte, ravageur., IntroductionThe mangrove ecosystem, found in intertidal zones of tropical and sub-tropical coasts (Thomas et al. 2017), plays a vital role in providing a variety of plant and animal products, as [...]

Laguncularia racemosa is widely planted in coastal mudflats as a pioneer species of mangrove afforestation in China; however, whether it exhibits invasiveness as an exotic species has been a topic of debate. In this study, we investigated the distribution, community structure, and population characteristics of L. racemosa on Hainan Island, China, to discuss its potential invasiveness. The results showed that Hainan Island has become an important distribution area for L. racemosa in China, covering a total area of 64.90 ha. In this investigation, a total of 11 true mangrove species, belonging to six families and 11 genera, were discovered in the L. racemosa community throughout Hainan Island. Furthermore, L. racemosa exhibited a strong adaptive range to seawater salinity and demonstrated a high capacity for natural dispersion. L. racemosa exhibited high importance values in the tree, shrub, and seedling layers of this artificial community, indicating its dominance and potential exclusion of other mangrove species. Over time, the importance values of L. racemosa in the tree and shrub layers initially decreased and then increased, while the opposite trend was observed in the seedling layer. Overall, the diversity indexes, including the Simpson index, Shannon–Wiener index, and Pielou community evenness index, were low in the planted L. racemosa forest on Hainan Island, suggesting a relatively simple species composition within the L. racemosa community. Additionally, based on the height levels of the L. racemosa population, we found that it mainly belonged to the first level, characterized by a large number of seedlings on Hainan Island. The number of L. racemosa seedlings gradually decreased in subsequent levels, and higher height levels of L. racemosa appeared with longer planting times, indicating a growing trend of potential invasiveness of L. racemosa on Hainan Island over an extended period. We suggest that the government should be able to list L. racemosa as an invasive species that can be harvested in the future. Based on this, this study provides fundamental data and theoretical references for the sustainable prevention, control, and management of the exotic species L. racemosa on Hainan Island, and also in other mangrove wetlands in China. [ABSTRACT FROM AUTHOR]

How plants adapt and diverge in extreme environments is a key question of plant evolution and ecology. Mangrove invasion of intertidal environments is facilitated by adaptive phenotypes such as aerial roots, salt‐secreting leaf, and viviparity, and genomic mechanisms including whole genome duplication and transposable element number reduction. However, a number of mangroves lack these typical phenotypes. The question we ask is whether these phenotypically atypical mangroves also have distinct genomic features? The sibling mangrove species Lumnitzera littorea and Lumnitzera racemosa provide a model to study this question. We sequenced and assembled their genomes to chromosome level, together with a closely related species Combretum micranthum. While most mangroves have small genomes, the genomes of both Lumnitzera species are large (1443 and 1317 Mb) and carry a high proportion of repeat sequences (~75%). Moreover, Lumnitzera species have not undergone post‐gamma whole‐genome duplications. Their genome size increased mainly due to the expansion of repeat sequences in their ancestors. However, Lumnitzera genomes have reduced transposable elements by constraining the proliferation of new LTR‐RTs. Meanwhile, the two species have more gene families contracted than expanded, and some gene families with reversed size change may underlie their differentiation in root morphology and local distribution. We identified 86 chromosomal inversions, five of which are measured between 6.5 and 12.8 megabases. A number of genes located in these inversions function in pigment biosynthesis, a process likely involved in flower colour differentiation between the Lumnitzera species. We conclude that the mangroves with atypical phenotypes also have atypical genomic evolution. [ABSTRACT FROM AUTHOR]

Whole‐genome duplication (WGD) is believed to increase the chance of adaptation to a new environment. This conjecture may apply particularly well to new environments that are not only different but also more variable than ancestral habitats. One such prominent environment is the interface between land and sea, which has been invaded by woody plants, collectively referred as mangroves, multiple times. Here, we use two distantly related mangrove species (Avicennia marina and Rhizophora apiculata) to explore the effects of WGD on the adaptive process. We found that a high proportion of duplicated genes retained after WGD have acquired derived differential expression in response to salt gradient treatment. The WGD duplicates differentially expressed in at least one copy usually (>90%) diverge from their paralogues' expression profiles. Furthermore, both species evolved in parallel to have one paralogue expressed at a high level in both fresh water and hypersaline conditions but at a lower level at medium salinity. The pattern contrasts with the conventional view of monotone increase/decrease as salinity increases. Differentially expressed copies have thus probably acquired a new role in salinity tolerance. Our results indicate that the WGD duplicates may have evolved to function collaboratively in coping with different salinity levels, rather than specializing in the intermediate salinity optimal for mangrove plants. In conclusion, WGD and the retained duplicates appear to be an effective solution for adaptation to new and unstable environments. see also the Perspective by Shawn K. Thomas, Hong An and J. Chris Pires [ABSTRACT FROM AUTHOR]

In the conventional view, species are separate gene pools delineated by reproductive isolation (RI). In an alternative view, species may also be delineated by a small set of 'speciation genes' without full RI, a view that has gained broad acceptance. A recent survey, however, suggested that the extensive literature on 'speciation with gene flow' is mostly (if not all) about exchanges in the early stages of speciation. There is no definitive evidence that the observed gene flow actually happened after speciation is completed. Here, we wish to know whether 'good species' (defined by the 'secondary sympatry' test) do continue to exchange genes and, importantly, under what conditions such exchanges can be observed. De novo whole-genome assembly and re-sequencing of individuals across the range of two closely related mangrove species (Rhizophora mucronata and R. stylosa) reveal the genomes to be well delineated in allopatry. They became sympatric in northeastern Australia but remain distinct species. Nevertheless, their genomes harbor ∼4000–10   000 introgression blocks averaging only about 3–4 Kb. These fine-grained introgressions indicate continual gene flow long after speciation as non-introgressable 'genomic islets,' ∼1.4 Kb in size, often harbor diverging genes of flower or gamete development. The fine-grained introgression in secondary sympatry may help settle the debate about sympatric vs. micro-allopatric speciation. In conclusion, true 'good species' may often continue to exchange genes but the opportunity for detection is highly constrained. [ABSTRACT FROM AUTHOR]

SUMMARY: Adaptation to new environments is a key evolutionary process which presumably involves complex genomic changes. Mangroves, a collection of approximately 80 woody plants that have independently invaded intertidal zones >20 times, are ideal for studying this process. We assembled near‐chromosome‐scale genomes of three Xylocarpus species as well as an outgroup species using single‐molecule real‐time sequencing. Phylogenomic analysis reveals two separate lineages, one with the mangrove Xylocarpus granatum and the other comprising a mangrove Xylocarpus moluccensis and a terrestrial Xylocarpus rumphii. In conjunction with previous studies, we identified several genomic features associated with mangroves: (i) signals of positive selection in genes related to salt tolerance and root development; (ii) genome‐wide elevated ratios of non‐synonymous to synonymous substitution relative to terrestrial relatives; and (iii) active elimination of long terminal repeats. These features are found in the terrestrial X. rumphii in addition to the two mangroves. These genomic features, not being strictly mangrove‐specific, are hence considered pre‐adaptive. We infer that the coastal but non‐intertidal habitat of X. rumphii may have predisposed the common ancestor to invasion of true mangrove habitats. Other features including the preferential retention of duplicated genes and intolerance to pseudogenization are not found in X. rumphii and are likely true adaptive features in mangroves. In conclusion, by studying adaptive shift and partial shifts among closely related species, we set up a framework to study genomic features that are acquired at different stages of the pre‐adaptation and adaptation to new environments. Significance Statement: We sequenced and assembled high‐quality genomes for three Xylocarpus species and one Swietenia species using single‐molecule real‐time sequencing. By illustrating genomic features acquired in different stages of the complex process of adapting to the extreme intertidal environments, we provide evidences for pre‐adaptation and adaptation in different stages of transition to a new environment [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Sequencing multiple species that share the same ecological niche may be a new frontier for genomic studies. While such studies should shed light on molecular convergence, genomic-level analyses have been unsuccessful, due mainly to the absence of empirical controls. Woody plant species that colonized the global tropical coasts, collectively referred to as mangroves, are ideal for convergence studies. Here, we sequenced the genomes/transcriptomes of 16 species belonging in three major mangrove clades. To detect convergence in a large phylogeny, a CCS+ model is implemented, extending the more limited CCS method (convergence at conservative sites). Using the empirical control for reference, the CCS+ model reduces the noises drastically, thus permitting the identification of 73 convergent genes with P true (probability of true convergence) > 0.9. Products of the convergent genes tend to be on the plasma membrane associated with salinity tolerance. Importantly, convergence is more often manifested at a higher level than at amino-acid (AA) sites. Relative to >50 plant species, mangroves strongly prefer 4 AAs and avoid 5 others across the genome. AA substitutions between mangrove species strongly reflect these tendencies. In conclusion, the selection of taxa, the number of species and, in particular, the empirical control are all crucial for detecting genome-wide convergence. We believe this large study of mangroves is the first successful attempt at detecting genome-wide site convergence. [ABSTRACT FROM AUTHOR]

Allopatric speciation requiring an unbroken period of geographical isolation has been the standard model of neo-Darwinism. While doubts have been repeatedly raised, strict allopatry without any gene flow remains a plausible mechanism in most cases. To rigorously reject strict allopatry, genomic sequences superimposed on the geological records of a well-delineated geographical barrier are necessary. The Strait of Malacca, narrowly connecting the Pacific and Indian Ocean coasts, serves at different times either as a geographical barrier or a conduit of gene flow for coastal/marine species. We surveyed 1700 plants from 29 populations of 5 common mangrove species by large-scale DNA sequencing and added several whole-genome assemblies. Speciation between the two oceans is driven by cycles of isolation and gene flow due to the fluctuations in sea level leading to the opening/closing of the Strait to ocean currents. Because the time required for speciation in mangroves is longer than the isolation phases, speciation in these mangroves has proceeded through many cycles of mixing-isolation-mixing, or MIM, cycles. The MIM mechanism, by relaxing the condition of no gene flow, can promote speciation in many more geographical features than strict allopatry can. Finally, the MIM mechanism of speciation is also efficient, potentially yielding m n (m  > 1) species after n cycles. [ABSTRACT FROM AUTHOR]

Abstract: The projected increases in sea levels are expected to affect coastal ecosystems. Tropical communities, anchored by mangrove trees and having experienced frequent past sea level changes, appear to be vibrant at present. However, any optimism about the resilience of these ecosystems is premature because the impact of past climate events may not be reflected in the current abundance. To assess the impact of historical sea level changes, we conducted an extensive genetic diversity survey on the Indo‐Malayan coast, a hotspot with a large global mangrove distribution. A survey of 26 populations in six species reveals extremely low genome‐wide nucleotide diversity and hence very small effective population sizes (Ne) in all populations. Whole‐genome sequencing of three mangrove species further shows the decline in Ne to be strongly associated with the speed of past changes in sea level. We also used a recent series of flooding events in Yalong Bay, southern China, to test the robustness of mangroves to sea level changes in relation to their genetic diversity. The events resulted in the death of half of the mangrove trees in this area. Significantly, less genetically diverse mangrove species suffered much greater destruction. The dieback was accompanied by a drastic reduction in local invertebrate biodiversity. We thus predict that tropical coastal communities will be seriously endangered as the global sea level rises. Well‐planned coastal development near mangrove forests will be essential to avert this crisis. [ABSTRACT FROM AUTHOR]

Abstract: Aim: The genus Xylocarpus contains two mangrove species, X. granatum and X. moluccensis, and a rare non‐mangrove, X. rumphii. The two mangrove species are ideal models to study the biogeography of coastal plants with a unique dispersal ability, that is via buoyant propagules. We constructed the phylogeny of Xylocarpus and its relatives and determined the population structures of the two mangrove species. We aimed to elucidate the roles of continental drift and long‐distance dispersal (LDD) in shaping the present‐day distribution of Xylocarpus and to determine the factors affecting the patterns of population differentiation. Location: The Indo‐West Pacific (IWP) region. Methods: Thirty populations of X. granatum, 15 of X. moluccensis and four of X. rumphii were sampled across the IWP region. Five chloroplast DNA intergenic spacers were sequenced for Xylocarpus and outgroup species to determine divergence times. The genetic diversity, divergence and structure of the two mangrove species were further analysed using five nuclear and two chloroplast DNA loci. Migrations between oceanic regions were estimated. Results: The genus Xylocarpus diverged from its sister genus Carapa approximately 19.4 Ma. The populations of X. granatum differentiated into three groups, with genetic breaks present across the Malay Peninsula and Wallacea, whereas X. moluccensis populations differentiated into two groups, with a genetic break present only across the Malay Peninsula. Migration was also observed between populations of the Southeast Asian and Australasian regions in X. moluccensis but not in X. granatum. Main conclusion: Since Xylocarpus originated after the breakup of Gondwana and subsequent plate motions, its current distribution range should have been facilitated by present‐day LDD instead of past continental drift. Despite the capacity of LDD, the presence of differing population structures across land barriers (the Sunda and Sahul Shelves) and ocean currents indicated differential limitations in the dispersal capabilities of X. granatum and X. moluccensis. [ABSTRACT FROM AUTHOR]

Avicennia L. (Avicenniaceae), one of the most diverse mangrove genera, is distributed widely in tropical and subtropical intertidal zones worldwide. Five species of Avicennia in the Indo-West Pacific region have been previously described. However, their phylogenetic relationships were determined based on morphological and allozyme data. To enhance our understanding of evolutionary patterns in the clade, we carried out a molecular phylogenetic study using wide sampling and multiple loci. Our results support two monophyletic clades across all species worldwide in Avicennia: an Atlantic-East Pacific (AEP) lineage and an Indo-West Pacific (IWP) lineage. This split is in line with biogeographic distribution of the clade. Focusing on the IWP branch, we reconstructed a detailed phylogenetic tree based on sequences from 25 nuclear genes. The results identified three distinct subclades, (1) A. rumphiana and A. alba, (2) A. officinalis and A. integra, and (3) the A. marina complex, with high bootstrap support. The results strongly corresponded to two morphological traits in floral structure: stigma position in relation to the anthers and style length. Using Bayesian dating methods we estimated diversification of the IWP lineage was dated to late Miocene (c. 6.0 million years ago) and may have been driven largely by the fluctuating sea levels since that time. [ABSTRACT FROM AUTHOR]

Aegiceras corniculatum (L.) Blanco is one of the most salt tolerant mangrove species and can thrive in 3% salinity at the seaward edge of mangrove forests. Here we sequenced the transcriptome of A. corniculatum used Illumina GA platform to develop its genomic resources for ecological and evolutionary studies. We obtained about 50 million high-quality paired-end reads with 75 bp in length. Using the short read assembler Velvet, we yielded 49,437 contigs with the average length of 625 bp. A total of 32,744 (66.23%) contigs showed significant similarity to the GenBank non-redundant (NR) protein database. 30,911 and 18,004 of these sequences were assigned to Gene Ontology and eukaryotic orthologous groups of proteins (KOG). A total of 4942 transcripts from our assemblies had significant similarity with KEGG Orthologs and were involved in 144 KEGG pathways, while 9899 unigenes had enzyme commission (EC) numbers. In addition, 9792 transcriptome-derived SSRs were identified from 7342 sequences. With our strict criteria, 4165 candidate SNPs were also identified from 2058 contigs. Some of these SNPs were further validated by Sanger sequencing. Genomic resources generated in this study should be valuable in ecological, evolutionary, and functional genomics studies for this mangrove species. [ABSTRACT FROM AUTHOR]

The genus Rhizophora is one of the most important components of mangrove forests. It is an ideal system for studying biogeography, molecular evolution, population genetics, hybridization and conservation genetics of mangroves. However, there are no sufficient molecular markers to address these topics. Here, we developed 77 pairs of nuclear gene primers, which showed successful PCR amplifications across all five Rhizophora species and sequencing in R. apiculata. Here, we present three tentative applications using a subset of the developed nuclear genes to (I) reconstruct the phylogeny, (II) examine the genetic structure and (III) identify natural hybridization in Rhizophora. Phylogenetic analyses support the hypothesis that Rhizophora had disappeared in the Atlantic-East Pacific (AEP) region and was re-colonized from the IWP region approximately 12.7 Mya. Population genetics analyses in four natural populations of R. apiculata in Hainan, China, revealed extremely low genetic diversity, strong population differentiation and extensive admixture, suggesting that the Pleistocene glaciations, particularly the last glacial maximum, greatly influenced the population dynamics of R. apiculata in Hainan. We also verified the hybrid status of a morphologically intermediate individual between R. apiculata and R. stylosa in Hainan. Based on the sequences of five nuclear genes and one chloroplast intergenic spacer, this individual is likely to be an F1 hybrid, with R. stylosa as its maternal parent. The nuclear gene markers developed in this study should be of great value for characterizing the hybridization and introgression patterns in other cases of this genus and testing the role of natural selection using population genomics approaches. [ABSTRACT FROM AUTHOR]

Mangroves are dominant woody plants in the intertidal zones and are of both ecological and economic importance. Species of Ceriops , also called yellow mangroves, have many adaptive traits (including vivipary) for coping with the harsh marine environments. However, little is known about the origination and evolutionary history of this genus. In this study, we aim to provide clues to these two questions by sequencing the transcriptomes of two Ceriops species, Ceriops tagal and Ceriops zippeliana , and one of their terrestrial relatives, Pellacalyx yunnanensis . 48.19, 10.50 and 35.37 million high-quality reads that were generated by Illumina sequencing were assembled into 50,807, 40,543 and 64,147 contigs for the three species, respectively. After removing redundancy and contigs with low coverage, 39,361, 34,362, and 51,668 contigs with the N50 values of 1553, 772 and 1833 bp, respectively, were retained for further analysis. Of them, 17,348, 16,484 and 18,038 contigs were successfully annotated with the known gene ontology (GO) terms. GO classifications of the transcriptome profiles for the three species are similar. Most of the contigs were assigned to the cell and organelle related GO terms in the cellular component category, “binding” in the molecular function category, and “cellular process”, “metabolic process” and “biological regulation” in the biological process category. We identified more than 6000 pairs of orthologs for each pair of the three species, with the peak of synonymous substitution rate (Ks) distribution of 0.03 between the two Ceriops species and 0.23 between each Ceriops species and P. yunnanensis . Our transcriptomic data provide a great amount of genomic resources for yellow mangroves and can be used for studying the origination and adaptive evolution of mangroves. [ABSTRACT FROM AUTHOR]

Mangroves are a group of unique plants anchoring in and well adapting to the extreme intertidal environment with high salinity, hypoxia and high temperature and ultraviolet (UV) radiation. Sonneratia caseolaris is a major mangrove tree widely distributed across the West-Indo Pacific region, however the genetic mechanisms of its adaptive evolution are still unclear. In the present study, we performed comparative transcriptome analyses between S. caseolaris and its two non-mangrove relatives, Trapa bispinosa and Duabanga grandiflora , to better understand the evolutionary adaptation of S. caseolaris . We obtained 39.92, 69.96 and 47.78 million high-quality paired-end reads using the Illumina platform and de novo assembled them into 47,954, 73,284 and 66,459 unigenes with low redundancy and high coverage. Of them, 20,181, 28,657 and 25,244 unigenes were successfully assigned to level-2 Gene Ontology (GO) terms, and we found the distribution of GO terms were similar among the three species. Approximate 56% unigenes were involved in “response to stimulus” in all three species. Furthermore, we identified 23 unigenes under positive selection in S. caseolaris , which may be crucial for adaptation of this mangrove species to the extreme intertidal environment. [ABSTRACT FROM AUTHOR]

Ecological restoration of mangrove ecosystems that became susceptible to recent habitat perturbations is crucial for tropical coast conservation. The white mangrove Laguncularia racemosa, a pioneer species inhabiting intertidal environments of the Atlantic East Pacific (AEP) region, has been used for reforestation in China for decades. However, the molecular mechanisms underlying its fast growth and high adaptive potential remain unknown. Using PacBio single‐molecule real‐time sequencing, we completed a high‐quality L. racemosa genome assembly covering 1105 Mb with scaffold N50 of 3.46 Mb. Genomic phylogeny shows that L. racemosa invaded intertidal zones during a period of global warming. Multi‐level genomic convergence analyses between L. racemosa and three native dominant mangrove clades show that they experienced convergent changes in genes involved in nutrient absorption and high salinity tolerance. This may explain successful L. racemosa adaptation to stressful intertidal environments after introduction. Without recent whole‐genome duplications or activated transposable elements, L. racemosa has retained many tandem gene duplications. Some of them are involved in auxin biosynthesis, intense light stress and cold stress response pathways, associated with L. racemosa's ability to grow fast under high light or cold conditions when used for reforestation. In summary, our study identifies shared mechanisms of intertidal environmental adaptation and unique genetic changes underlying fast growth in mangrove‐unfavourable conditions and sheds light on the molecular mechanisms of the white mangrove utility in ecological restoration. [ABSTRACT FROM AUTHOR]

Terpene synthases (TPSs) play a crucial role in the synthesis of terpenoids that contribute to the scent profiles of flowers. However, few studies report the genome-wide analysis of TPS s gene in Jasminum sambac var. Fuzhou bifoliatum and their expression pattern in response to methyl jasmonate (MeJA). In this study, we employed bioinformatics tools for genome-wide analysis of the J . sambac TPS (DJTPS) gene family and determined the physical and chemical properties, subcellular location, protein-protein interactions, phylogenetic relationship, subfamily classification, chromosomal location and collinearity, gene structure, conserved motifs, and promoter cis -acting elements. The expression patterns of DJTPS s in different tissues and in response to MeJA treatment were analyzed based on the transcriptome data combined with quantitative real-time PCR (qRT-PCR). We identified 32 intact DJTPS genes in the genome of J . sambac , which presented uneven distribution across nine chromosomes. All the deduced proteins were hydrophilic, predominantly localized in the cytoplasm. The phylogenetic analysis classified the DJTPS genes into five subfamilies: TPS-a, TPS-b, TPS-c, TPS-e/f, and TPS-g. The results of the collinearity analysis showed a total of 10 sets of replication events in DJTPS s, most of which underwent purifying selection. A comparative analysis of TPS homologous gene pairs was performed among J . sambac var. Fuzhou bifoliatum and other six species, which revealed different number of homologous gene pairs. The number of exons and motifs was conserved within the same subfamily. DJTPS genes carried multiple elements that may be involved in the response to MeJA. In addition, the transcriptome and qRT-PCR data unveiled that several TPS genes exhibited tissue-specific expression patterns, and the genes with specific expression in flowers were the most. Upon exposure to MeJA, 14 TPS genes showcased upregulated expression 5 h or 6 h post-treatment, and DJTPS03 , DJTPS04 and DJTPS21 showed significantly increased expression levels after MeJA treatment. This study provides preliminary evidence that MeJA possesses the ability to enhance the expression of DJTPS genes during the critical flowering stage, which will facilitate the synthesis of terpenoids and improve the quality of floral fragrance.

The haptophyte Isochrysis galbana is considered as a promising source for food supplements due to its rich fucoxanthin and polyunsaturated fatty acids content. Here, the I. galbana mitochondrial genome (mitogenome) was sequenced using a combination of Illumina and PacBio sequencing platforms. This 39,258 bp circular mitogenome has a total of 46 genes, including 20 protein-coding genes, 24 tRNA genes and two rRNA genes. A large block of repeats (~12.7 kb) was segregated in one region of the mitogenome, accounting for almost one third of the total size. A trans -spliced gene cox1 was first identified in I. galbana mitogenome and was verified by RNA-seq and DNA-seq data. The massive expansion of tandem repeat size and cis - to trans -splicing shift could be explained by the high mitogenome rearrangement rates in haptophytes. Strict SNP calling based on deep transcriptome sequencing data suggested the lack of RNA editing in both organelles in this species, consistent with previous studies in other algal lineages. To gain insight into haptophyte mitogenome evolution, a comparative analysis of mitogenomes within haptophytes and among eight main algal lineages was performed. A core gene set of 15 energy and metabolism genes is present in haptophyte mitogenomes, consisting of 1 cob , 3 cox , 7 nad , 2 atp and 2 ribosomal genes. Gene content and order was poorly conserved in this lineage. Haptophyte mitogenomes have lost many functional genes found in many other eukaryotes including rps / rpl , sdh , tat , secY genes, which make it contain the smallest gene set among all algal taxa. All these implied the rapid-evolving and more recently evolved mitogenomes of haptophytes compared to other algal lineages. The phylogenetic tree constructed by cox1 genes of 204 algal mitogenomes yielded well-resolved internal relationships, providing new evidence for red-lineages that contained plastids of red algal secondary endosymbiotic origin. This newly assembled mitogenome will add to our knowledge of general trends in algal mitogenome evolution within haptophytes and among different algal taxa., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Fang, Xu, Chen, Lin, Lin, Lei, Zhong, Huang and He.)

Sesuvium portulacastrum has a strong salt tolerance and can grow in saline and alkaline coastal and inland habitats. This study investigated the physiological and molecular responses of S. portulacastrum to high salinity by analyzing the changes in plant phytohormones and antioxidant activity, including their differentially expressed genes (DEGs) under similar high-salinity conditions. High salinity significantly affected proline (Pro) and hydrogen peroxide (H 2 O 2 ) in S. portulacastrum seedlings, increasing Pro and H 2 O 2 contents by 290.56 and 83.36%, respectively, compared to the control. Antioxidant activities, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), significantly increased by 83.05, 205.14, and 751.87%, respectively, under high salinity. Meanwhile, abscisic acid (ABA) and gibberellic acid (GA 3 ) contents showed the reverse trend of high salt treatment. De novo transcriptome analysis showed that 36,676 unigenes were matched, and 3,622 salt stress-induced DEGs were identified as being associated with the metabolic and biological regulation processes of antioxidant activity and plant phytohormones. POD and SOD were upregulated under high-salinity conditions. In addition, the transcription levels of genes involved in auxin ( SAURs and GH3 ), ethylene ( ERF1 , ERF3 , ERF114 , and ABR1 ), ABA ( PP2C ), and GA 3 ( PIF3 ) transport or signaling were altered. This study identified key metabolic and biological processes and putative genes involved in the high salt tolerance of S. portulacastrum and it is of great significance for identifying new salt-tolerant genes to promote ecological restoration of the coastal strand., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Chen, Zhou, Cai, Feng, Zhong, Fang and Zhang.)

Sonneratia caseolaris is a native mangrove species found in China. It is fast growing and highly adaptable for mangrove afforestation, but suffered great damage by chilling event once introduced to high latitude area. To understand the response mechanisms under chilling stress, physiological and transcriptomic analyses were conducted. The relative electrolyte conductivity, malondialdehyde (MDA) content, soluble sugar content and soluble protein content increased significantly under chilling stress. This indicated that S. caseolaris suffered great damage and increased the levels of osmoprotectants in response to the chilling stress. Gene expression comparison analysis of S. caseolaris leaves after 6 h of chilling stress was performed at the transcriptional scale using RNA-Seq. A total of 168,473 unigenes and 3,706 differentially expressed genes (DEGs) were identified. GO and KEGG enrichment analyses showed that the DEGs were mainly involved in carbohydrate metabolism, antioxidant enzyme, plant hormone signal transduction, and transcription factors (TFs). Sixteen genes associated with carbohydrate metabolism, antioxidant enzyme, phytohormones and TFs were selected for qRT-PCR verification, and they indicated that the transcriptome data were reliable. Our work provided a comprehensive review of the chilling response of S. caseolaris at both physiological and transcriptomic levels, which will prove useful for further studies on stress-responses in mangrove plants., Competing Interests: The authors declare there are no competing interests., (©2021 Yang et al.)

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., (Cairong Zhong, Donglin Li, Ying Zhang.)

Mangroves invade some very marginal habitats for woody plants-at the interface between land and sea. Since mangroves anchor tropical coastal communities globally, their origin, diversification and adaptation are of scientific significance, particularly at a time of global climate change. In this study, a combination of single-molecule long reads and the more conventional short reads are generated from Rhizophora apiculata for the de novo assembly of its genome to a near chromosome level. The longest scaffold, N50 and N90 for the R. apiculata genome, are 13.3 Mb, 5.4 Mb and 1.0 Mb, respectively. Short reads for the genomes and transcriptomes of eight related species are also generated. We find that the ancestor of Rhizophoreae experienced a whole-genome duplication ~70 Myrs ago, which is followed rather quickly by colonization and species diversification. Mangroves exhibit pan-exome modifications of amino acid (AA) usage as well as unusual AA substitutions among closely related species. The usage and substitution of AAs, unique among plants surveyed, is correlated with the rapid evolution of proteins in mangroves. A small subset of these substitutions is associated with mangroves' highly specialized traits (vivipary and red bark) thought to be adaptive in the intertidal habitats. Despite the many adaptive features, mangroves are among the least genetically diverse plants, likely the result of continual habitat turnovers caused by repeated rises and falls of sea level in the geologically recent past. Mangrove genomes thus inform about their past evolutionary success as well as portend a possibly difficult future.

Background: A large-scale systematical investigation of the influence of Pleistocene climate oscillation on mangrove population dynamics could enrich our knowledge about the evolutionary history during times of historical climate change, which in turn may provide important information for their conservation., Results: In this study, phylogeography of a mangrove tree Sonneratia alba was studied by sequencing three chloroplast fragments and seven nuclear genes. A low level of genetic diversity at the population level was detected across its range, especially at the range margins, which was mainly attributed to the steep sea-level drop and associated climate fluctuations during the Pleistocene glacial periods. Extremely small effective population size (Ne) was inferred in populations from both eastern and western Malay Peninsula (44 and 396, respectively), mirroring the fragility of mangrove plants and their paucity of robustness against future climate perturbations and human activity. Two major genetic lineages of high divergence were identified in the two mangrove biodiversity centres: the Indo-Malesia and Australasia regions. The estimated splitting time between these two lineages was 3.153 million year ago (MYA), suggesting a role for pre-Pleistocene events in shaping the major diversity patterns of mangrove species. Within the Indo-Malesia region, a subdivision was implicated between the South China Sea (SCS) and the remaining area with a divergence time of 1.874 MYA, corresponding to glacial vicariance when the emerged Sunda Shelf halted genetic exchange between the western and eastern coasts of the Malay Peninsula during Pleistocene sea-level drops. Notably, genetic admixture was observed in populations at the boundary regions, especially in the two populations near the Malacca Strait, indicating secondary contact between divergent lineages during interglacial periods. These interregional genetic exchanges provided ample opportunity for the re-use of standing genetic variation, which could facilitate mangrove establishment and adaptation in new habitats, especially in the context of global climate changes., Conclusion: Phylogeogrpahic analysis in this study reveal that Pleistocene sea-level fluctuations had profound influence on population differentiation of the mangrove tree S. alba. Our study highlights the fragility of mangrove plants and offers a guide for the conservation of coastal mangrove communities experiencing ongoing changes in sea-level.