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.

Spectral Reflectance-Based Mangrove Species Mapping from WorldView-2 Imagery of Karimunjawa and Kemujan Island, Central Java Province, Indonesia

Mangrove mapping at the species level enables the creation of a detailed inventory of mangrove forest biodiversity and supports coastal ecosystem management. The Karimunjawa National Park in Central Java Province is one of Indonesia’s mangrove habitats with high biodiversity, namely, 44 species representing 25 true mangroves and 19 mangrove associates. This study aims to (1) classify and group mangrove species by their spectral reflectance characteristics, (2) map mangrove species by applying their spectral reflectance to WorldView-2 satellite imagery with the spectral angle mapper (SAM), spectral information divergence (SID), and spectral feature fitting (SFF) algorithms, and (3) assess the accuracy of the produced mangrove species mapping of the Karimunjawa and Kemujan Islands. The collected field data included (1) mangrove species identification, (2) coordinate locations of targeted mangrove species, and (3) the spectral reflectance of mangrove species measured with a field spectrometer. Dendrogram analysis was conducted with the Ward linkage method to classify mangrove species based on the distance between the closest clusters of spectral reflectance patterns. The dendrogram showed that the 24 mangrove species found in the field could be grouped into four levels. They consisted of two, four, and five species groups for Levels 1 to 3, respectively, and individual species for Level 4. The mapping results indicated that the SID algorithm had the highest overall accuracy (OA) at 49.72%, 22.60%, and 15.20% for Levels 1 to 3, respectively, while SFF produced the most accurate results for individual species mapping (Level 4) with an OA of 5.08%. The results suggest that the greater the number of classes to be mapped, the lower the mapping accuracy. The results can be used to model the spatial distribution of mangrove species or the composition of mangrove forests and update databases related to coastal management.

Optimizing mangrove conservation efforts with improved understanding of phytosociology-ecology synergy in Sri Lanka

The study aimed to understand the forest structure and ecological factors influencing mangrove distribution in eight mangrove forests across three climatic zones in Sri Lanka. We studied mangrove diversity and vegetation structure with 10m wide belt transects laid of different lengths (n=96) across the land-water gradient. Mangroves along the transect were identified, enumerated, and measured diameter at breast height (DBH). Subsurface water samples were taken in the adjoining lagoon/estuary to assess the environmental parameters (n=144), and water quality parameters were measured. Site-dependent spatial changes in the community structure were depicted through cluster analysis (CA). The forest survey revealed a heterogeneous mixture of 20 true mangrove species across the sites dominated by Avicennia, Rhizophora, and Sonneratia spp. Among the several environmental parameters analyzed by the distance-based redundancy ordination analysis (dbRDA), salinity, dissolved oxygen, and precipitation were found to be controlling factors in mangrove community structure. In addition, discriminant analysis confirmed the presence of ecological-phytosociological influence on mangrove assemblages identified through CA. The significant structural parameters tree density, and taxonomic diversity when tested using the canonical analysis of principal coordinates (CAP), altered the species abundance across the sites surveyed. The results suggest that there is a strong linkage between phytosociology and ecology with the mangrove forest distribution and this relationship needs to be considered wisely to fortify successful restoration practices.

Establishing community-wide DNA barcode references for conserving mangrove forests in China

Background Mangrove ecosystems have been the focus of global attention for their crucial role in sheltering coastal communities and retarding global climate change by sequestering ‘blue carbon’. China is relatively rich in mangrove diversity, with one-third of the ca. 70 true mangrove species and a number of mangrove associate species occurring naturally along the country’s coasts. Mangrove ecosystems, however, are widely threatened by intensifying human disturbances and rising sea levels. DNA barcoding technology may help protect mangrove ecosystems by providing rapid species identification. Results To investigate this potential, 898 plant specimens were collected from 33 major mangrove sites in China. Based on the morphologic diagnosis, the specimens were assigned to 72 species, including all 28 true mangrove species and all 12 mangrove associate species recorded in China. Three chloroplast DNA markers rbcL, trnH-psbA, matK, and one nuclear marker ITS2 were chosen to investigate the utility of using barcoding to identify these species. According to the criteria of barcoding gaps in genetic distance, sequence similarity, and phylogenetic monophyly, we propose that a single marker, ITS2, is sufficient to barcode the species of mangroves and their associates in China. Furthermore, rbcL or trnH-psbA can also be used to gather supplement confirming data. In using these barcodes, we revealed a very low level of genetic variation among geographic locations in the mangrove species, which is an alert to their vulnerability to climate and anthropogenic disturbances. Conclusion We suggest using ITS2 to barcode mangrove species and terrestrial coastal plants in South China. The DNA barcode sequences we obtained would be valuable in monitoring biodiversity and the restoration of ecosystems, which are essential for mangrove conservation.

Status and perspectives of mangrove management in Côte d'Ivoire

Mangroves are ecosystems characteristic of intertidal zones in tropical and subtropical regions. Rhizophora racemosa, Avicennia germinans and Conocarpus erectus are characteristic mangrove species found in Côte d'Ivoire. These mangroves could disappear without being fully studied due to the strong anthropic pressure. This study therefore proposes to establish a detailed cartography of the mangroves reported in Côte d'Ivoire and to model their potential distribution. Mangroves cover approximately 57.92 km², ie a linear coverage of 20.11% of the 540.14 km of coastline. The extent of these mangroves also decreased by 4.91 km² between 1996 and 2016. The maximum entropy model presents low-altitude coastal areas with high rainfall as well as average sunshine as favorable to mangroves. The particular ecological characteristic of mangroves as well as their particular mode of operation deserve to be taken into account in studies of flora in Côte d'Ivoire. It is therefore opportune to consider larger studies focusing specifically on the mangroves present in Ivory.

A preliminary investigation of endophytic fungal diversity at Hope, East Coast Demerara, Guyana

Foliar endophytic fungi spend a part of their life cycle on the leaves of plants. They may demonstrate no apparent symptoms but may also cause disease at a later time in the plant’s life. Studies investigating foliar fungal endophytes of mangroves are limited. Therefore, the purpose of this study was to investigate the foliar fungal endophytes present on the leaves of three mangrove species: namely Red mangrove (Rhizophora mangle), Black mangrove (Avicennia germinans) and White mangrove (Laguncularia racemosa). The study site was an area located at Hope, East Coast Demerara, and South America, Guyana. Out of sixty (60) leaf samples that were prepared, fourteen (14) fungal isolates were identified. Most of the fungi isolated in the study were found to be Hyphomycetes (Aspergillus, Fusarium, Penicillium, Alternaria, Cladosporium and Curvularia) while the others were Zygomorphic (Mucor and Rhizopus). The ANOVA calculations for the isolates from the three mangrove species were found to not be statistically significant. R mangle was the preferred host out of the three (3) species. The findings of this study confirm that mangroves have rich endophytic diversity and demonstrate rich research and biochemical potential.