Drought stress is a bottleneck factor for plant growth and development, especially in epiphytic orchids that absorb moisture mainly from the air. Recent studies have suggested that there are complex transcriptional regulatory networks related to drought stress in Dendrobium sinense. In this study, the transcription and metabolite alterations involved in drought stress response in D. sinense were investigated through RNA-seq and metabolomics. A total of 856 metabolites were identified from stressed and control samples, with 391 metabolites showing significant differences. With PacBio and Illumina RNA sequencing, 72,969 genes were obtained with a mean length of 2,486 bp, and 622 differentially expressed genes (DEGs) were identified. Correlation analysis showed 7 differential genes, and 39 differential metabolites were involved in interaction networks. The network analysis of differential genes and metabolites suggested that the pathways of purine metabolism and phenylpropanoid biosynthesis may play an important role in drought response in D. sinense. These results provide new insights and reference data for culturally important medicinal plants and the protection of endangered orchids.

Phalaenopsis cultivar ‘Panda’ is a beautiful and valuable ornamental for its big flower and unique big spots on the petals and sepals. Although anthocyanins are known as the main pigments responsible for flower colors in Phalaenopsis, and the anthocyanins biosynthetic pathway in Phalaenopsis is generally well known, the detailed knowledge of anthocynins regulation within the spot and non-spot parts in ‘Panda’ flower is limited. In this study, transcriptome and small RNA libraries analysis from spot and non-spot sepal tissues of ‘Panda’ were performed, and we found PeMYB7, PeMYB11, and miR156g, miR858 is associated with the purple spot patterning in its sepals. Transcriptome analyses showed a total 674 differentially expressed genes (DEGs), with 424 downregulated and 250 upregulated (Non-spot-VS-Spot), and 10 candidate DEGs involved in anthocyanin biosynthetic pathway. The qPCR analysis confirmed that seven candidate structure genes (PeANS, PeF3′H, PeC4H, PeF3H, PeF3H1, Pe4CL2, and PeCHI) have significantly higher expressing levels in spot tissues than non-spot tissues. A total 1552 differentially expressed miRNAs (DEMs) were detected with 676 downregulated and 876 upregulated. However, microRNA data showed no DEMs targeting on anthocyanin biosynthesis structure gene, while a total 40 DEMs target transcription factor (TF) genes, which expressed significantly different level in spot via non-spot sepal, including 2 key MYB regulator genes. These results indicated that the lack of anthocyanidins in non-spot sepal may not directly be caused by microRNA suppressing anthocyanidin synthesis genes rather than the MYB genes. Our findings will help in understanding the role of miRNA molecular mechanisms in the spot formation pattern of Phalaenopsis, and would be useful to provide a reference to similar research in other species.

Background: Gene flow in plants via pollen and seeds is asymmetrical at different geographic scales. Orchid seeds are adapted to long-distance wind dispersal but pollinium transfer is often influenced by pollinator behavior. We combined field studies with an analysis of genetic diversity among 155 physically mapped adults and 1105 F1 seedlings to evaluate the relative contribution of pollen and seed dispersal to overall gene flow among three sub-populations of the food-deceptive orchidPhalaenopsis pulcherrimaon Hainan Island, China.Results: Phalaenopsis pulcherrimais self-sterile and predominantly outcrossing, resulting in high population-level genetic diversity, but plants are clumped and exhibit fine-scale genetic structuring. Even so, we detected low differentiation among sub-populations, with polynomial regression analysis suggesting gene flow via seed to be more restricted than that via pollen. Paternity analysis confirmed capsules ofP. pulcherrimato each be sired by a single pollen donor, probably in part facilitated by post-pollination stigma obfuscation, with a mean pollen flow distance of 272.7 m. Despite limited sampling, we detected no loss of genetic diversity from one generation to the next.Conclusions: Outcrossing mediated by deceptive pollination and self-sterility promote high genetic diversity inP. pulcherrima. Long-range pollinia transfer ensures connectivity among sub-populations, offsetting the risk of genetic erosion at local scales.

Mangrove ecosystems play a dominant role in global, tropical, and subtropical coastal wetlands. Remote sensing plays a central role in mangrove conservation, as it is the preferred tool for monitoring changes in spatiotemporal distribution. To improve correlated estimation accuracies and explore the influencing mechanisms based on the mangrove ground survey, this study used a support vector machine (SVM) machine learning and Res-UNet deep learning algorithms to identify the land area of mangrove forests and the crown surface cover area of mangrove forests in the Hainan Island from 1991 to 2021. Both classification techniques were verified by a confusion matrix, which from 1991 to 2021, revealed overall accuracies of 93.11 ± 1.54% and 96.43 ± 1.15% for SVM and Res-UNet, respectively. Res-UNet was more accurate in identifying the crown surface cover area, whereas SVM was more suitable for obtaining the land area. Furthermore, based on the crown surface cover area of the mangrove forests on the Hainan Island, influencing mechanisms were analyzed through dynamic changes and landscape patterns. Since 1991, the Hainan Island mangrove forest area has increased, with the center of mass moving from coastal areas to the ocean and increasing the overall landscape fragmentation. Moreover, the change in the mangrove forests area was correlated with economic development and the increasingly urban population of the entire island. Altogether, the reliable assessment of the tropical mangrove forest land area and crown surface cover provides an important research foundation for the protection and restoration plans of tropical mangrove forests.

N⁶-methyladenine (6mA) DNA modification has been detected in several eukaryotic organisms, where it plays important roles in gene regulation and epigenetic memory maintenance. However, the genome-wide distribution patterns and potential functions of 6mA DNA modification in woodland strawberry (Fragaria vesca) remain largely unknown. Here, we examined the 6mA landscape in the F. vesca genome by adopting single-molecule real-time sequencing technology and found that 6mA modification sites were broadly distributed across the woodland strawberry genome. The pattern of 6mA distribution in the long non-coding RNA was significantly different from that in protein-coding genes. The 6mA modification influenced the gene transcription and was positively associated with gene expression, which was validated by computational and experimental analyses. Our study provides new insights into the DNA methylation in F. vesca.

Dendrobium sinense, an endemic medicinal herb in Hainan Island, is rich in bibenzyls. However, the key rate-limited enzyme involved in bibenzyl biosynthesis has yet to be identified in D. sinense. In this study, to explore whether there is a significant difference between the D. sinense tissues, the total contents of bibenzyls were determined in roots, pseudobulbs, and leaves. The results indicated that roots had higher bibenzyl content than pseudobulbs and leaves. Subsequently, transcriptomic sequencings were conducted to excavate the genes encoding type III polyketide synthase (PKS). A total of six D. sinense PKS (DsPKS) genes were identified according to gene function annotation. Phylogenetic analysis classified the type III DsPKS genes into three groups. Importantly, the c93636.graph_c0 was clustered into bibenzyl synthase (BBS) group, named as D. sinense BBS (DsBBS). The expression analysis by FPKM and RT-qPCR indicated that DsBBS showed the highest expression levels in roots, displaying a positive correlation with bibenzyl contents in different tissues. Thus, the recombinant DsBBS-HisTag protein was constructed and expressed to study its catalytic activity. The molecular weight of the recombinant protein was verified to be approximately 45 kDa. Enzyme activity analysis indicated that the recombinant DsBBS-HisTag protein could use 4-coumaryol-CoA and malonyl-CoA as substrates for resveratrol production in vitro. The Vmax of the recombinant protein for the resveratrol production was 0.88 ± 0.07 pmol s⁻¹ mg⁻¹. These results improve our understanding with respect to the process of bibenzyl biosynthesis in D. sinense.