Phyla nodiflora (L.) Greene, a perennial herbaceous vine belonging to the Verbenaceae family, is widely distributed in tropical and subtropical coastal regions. It is noted for its remarkable tolerance to salt and barren sandy soils. Additionally, Phyla nodiflora possesses strong covering ability, disease resistance, and adaptability, making it resilient to the harsh conditions of tropical coral islands, such as high temperatures, intense sunlight, and high salinity, where it rarely withers or degrades. Furthermore, Phyla nodiflora demonstrates robust resistance to exotic plant invasions, significantly reducing the presence of harmful plants within its growing area. Due to these advantages, Phyla nodiflora has been widely used in vegetation restoration on tropical coral islands in recent years. However, the molecular mechanism underlying its tolerance to extreme environments, such as salt stress, remained unknown.

Recently, a research team led by Xuncheng Liu and Nan Liu from the South China Botanical Garden, Chinese Academy of Sciences, published a research paper titled "Multi-omics analyses provide insights into the molecular basis for salt tolerance of Phyla nodiflora" in The Plant Journal, a prestigious botany journal. The research team employed second- and third-generation sequencing technologies combined with chromosome conformation capture techniques to assemble the genome of Phyla nodiflora at the chromosome level. The assembled genome spans 403.07 Mb, with 95.35% of the sequences anchored to 18 chromosomes. Genomic evolutionary analysis revealed that Phyla nodiflora has undergone two whole-genome duplication events, during which genes related to environmental adaptability and secondary metabolite synthesis have undergone significant expansion. Transcriptome analysis showed that the expansion and overexpression of genes involved in hormone synthesis and signaling, as well as ion transport, play crucial roles in the salt tolerance of Phyla nodiflora. Notably, the ZEP gene family, encoding zeaxanthin epoxidase (a key enzyme in carotenoid metabolism and abscisic acid (ABA) biosynthesis), has expanded significantly (eight times that of the model plant Arabidopsis thaliana) and its expression level increases markedly under salt stress. This finding is closely related to the maintenance of high ABA levels in Phyla nodiflora for an extended period after salt stress. Genetic and biochemical analyses demonstrated that overexpressing representative ZEP genes promotes ABA biosynthesis in plants and enhances their salt tolerance.

Based on the genomic data, the research team further conducted proteome and lysine acetylation modification omics analyses on Phyla nodiflora under salt stress. The study found that salt stress caused significant deacetylation changes in numerous genes involved in signal transduction, carbohydrate transport and metabolism, and transcriptional regulation. Functional analysis of acetylation modifications revealed that the 250th lysine residue (K250) of glutathione S-transferase (GST), which plays a crucial role in oxidative stress responses, underwent notable deacetylation after salt stress. Further research confirmed that deacetylation at the K250 site significantly enhanced the antioxidant enzyme activity of GST, thereby reducing the accumulation of reactive oxygen species in plants and enhancing their tolerance to salt stress.

Integrating the results of genomic, transcriptome, and acetylation analyses, the research team constructed a molecular network for Phyla nodiflora's response to salt stress: 1) At the genomic level, gene expansion resulting from two whole-genome duplications, particularly the increase in ABA synthesis-related genes (e.g., ZEP), lays the foundation for salt tolerance; 2) At the transcriptional level, salt stress activates the expression of numerous genes related to ABA signaling and ion transport while inhibiting growth and development-related genes, achieving a "stress-priority" resource allocation; 3) At the protein modification level, extensive protein deacetylation, particularly deacetylation of antioxidant enzymes such as GST, rapidly regulates protein activity in response to oxidative stress. This multi-layered and comprehensive regulatory mechanism enables Phyla nodiflora to survive and remain vigorous in high-salinity environments.

Xuncheng Liu and Nan Liu, are the corresponding authors of the paper, while Liyuan Wang, a jointly trained postdoctoral researcher, is the first author. Shuguang Jian (researcher), Feng Zheng (assistant researcher), and doctoral student Yuheng Zhou also participated in the research. This study was funded by the National Key Research and Development Program, the National Natural Science Foundation of China, the Guangdong Provincial Science and Technology Plan, and the Guangzhou Science and Technology Project. Paper link: http://dx.doi.org/10.1111/tpj.70325

Key words: acetylome; genome; salt stress; transcriptome; Phyla nodiflora‌

Abstract: Phyla nodiflora possesses natural resistance to multiple abiotic stresses, the mechanism underlying its tolerance to environmental stresses, such as salinity, is almost entirely unknown. In present work, our genomic, transcriptomic and lysine acetylomic analyses provide profound insight into the molecular basis of the adaption of Phyla nodiflora to salt stress

Figure. Molecular mechanism of Phyla nodiflora‌ in adapt to salt stress.