Ulmus pumila L. ‘Zhonghua Jinye’ is a plant variety with colourful leaves that is widely used in landscaping. In our study, the leaves of U. pumila ‘Zhonghua Jinye’ fade and turn green under light (LT, 45%), moderate (MD, 70%) and high (HG, 95%) shading treatment, reducing its ornamental value. However, the mechanism underlying this adaptation to shade is poorly understood. The objective of this study was to elucidate the mechanism of physiological, cellular microstructural and transcriptional changes involved in leaf regreening in U. pumila ‘Zhonghua Jinye’. Our results showed that the pigment content of U. pumila ‘Zhonghua Jinye’ leaves increased under shade stress, with a corresponding colour change from yellow to dark green. Thus, U. pumila ‘Zhonghua Jinye’ adapted to shade stress by increasing leaf pigment and chlorophyll content. Transmission electron microscopy showed that thylakoid stacking in the grana lamellae changed significantly from a loose state to a closely packed structure under shaded conditions. Because plant pigments were located mainly in thylakoids, this closer stacking increased photosynthetic efficiency and pigment accumulation. RNA sequencing analysis showed that Lhcb1, a key thylakoid membrane gene, was upregulated under shade, which promoted thylakoid stacking and light absorption. In the chlorophyll synthesis pathway, haeme metabolism was inhibited, increasing protoporphyrin IX flow to the chlorophyll pathway and promoting the synthesis of chlorophyll a/b. The simultaneous upregulation of plant hormone-related genes promoted an increase in plant leaf area, improving the light energy utilisation ratio. This study is the first to report the self-regulatory mechanism that leads to colour change in U. pumila ‘Zhonghua Jinye’ under shade stress and provides a theoretical basis for the cultivation of tree species with colourful leaves.

Melatonin, a potent endogenous antioxidant, holds promise for enhancing stress tolerance in woody plants, yet its molecular mechanism under saline–alkali stress remains poorly understood. This study systematically investigated the effects of exogenous melatonin on Ulmus pumila ‘Zhonghua Jinye’ by integrating physiological assays, transcriptomics, and metabolomics. Two-year-old cuttings were subjected to 150 mmol·L⁻¹ saline–alkali stress and treated with varying melatonin concentrations (0, 50, 100, 200, 400 μmol·L⁻¹; three replicates). Physiological evaluations identified 100 μmol·L⁻¹ melatonin (SMT100) as optimal, significantly enhancing antioxidant enzyme activities (SOD, CAT, APX, GR) by 28.7–41.5% and reducing reactive oxygen species (H₂O₂ by 31.5%; O_2⁻ by 38.2%) compared to untreated stressed controls. Integrated omics analysis (CK, S, SMT100 groups) revealed that saline–alkali stress suppressed the flavonoid biosynthesis pathway, down-regulating key genes such as UpANS1 (10.74-fold), UpANS2, UpHCT1, and UpDFR2, thereby reducing the accumulation of protective flavonoids like quercetin and kaempferol. Conversely, melatonin treatment reactivated this pathway, significantly up-regulating UpANS1 (17.36-fold induction), UpDFR2 (5.55-fold), UpCHS1, UpF3H6, and UpLAR2. This genetic reconfiguration promoted the synthesis of antioxidant flavonoids, enhancing the plant’s overall stress resilience, thus identifying UpANS1 as candidates associated with treatment response. The study provides a scientific basis for cultivating U. pumila ‘Zhonghua Jinye’ in saline–alkali soils and clarifies the molecular mechanism by which melatonin alleviates combined saline–alkali stress via flavonoid pathway regulation.

Introduction: The Malvaceae family shows rich species diversity and has substantial economic and medicinal value. However, the frequent interspecific hybridization among members of this family has resulted in confused phylogenetic relationships among the groups, limiting the usefulness of traditional classification methods. Methods: This study aimed to investigate the phylogenetic relationships among selected taxa of Malvaceae by evaluating 23 chloroplast (CP) genomes, including three newly assembled CP genomes. Among these three genomes, the CP genome of Hibiscus schizopetalus L. was reported for the first time, while the CP genomes of Alcea rosea L. and Hibiscus grewiifolius L., which have been deposited in NCBI, were re-analyzed here alongside newly generated data for comparative purposes. In addition, 20 downloaded CP genomes encompassing 13 genera were analyzed using SNPs in whole CP genomes data. Results: The results showed that the genomes ranged from 160,403 to 161,978 base pairs in length and consisted of small single copies (SSCs) and large single copies (LSCs) separated by two inverted repeat sequences (IRs), forming a typical quadripartite circular structure. The entire genome sequence showed relative conservation across species in terms of structure, GC content, codon usage, and gene composition. The mutation sites were mainly located in the LSC and SSC regions, and the variability in the non-coding regions was higher than that in the coding regions. The nucleotide polymorphism (Pi) analysis identified the non-coding regions such as ndhF-rpl32 and psbZ-trnG as high variable hotspots. A maximum likelihood phylogenetic tree was constructed based on SNPs in whole CP genomes data. The phylogenetic analysis divided these 23 species into five highly supported clades. It also revealed a close sister-group relationship between Abelmoschus and Hibiscus species, suggesting that Hibiscus may have a separate lineage from okra species. Discussion: In conclusion, the increasing availability of CP genome resources will enhance our understanding of the classification and evolutionary patterns of the Malvaceae family. The development of molecular markers will provide important molecular evidence for precise identification and classification revision of plants in this family.