Shuangyu Zhang’s research while affiliated with Northwest A&F University and other places

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Publications (15)


Designing Age-Friendly Paved Open Spaces: Key Green Infrastructure Features for Promoting Seniors’ Physical Activity
  • Article

June 2025

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5 Reads

Wei Dong

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Shuangyu Zhang

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[...]

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Guangkui Wang

Urban parks, key components of green infrastructure (GI), offer paved open spaces that significantly impact physical activity (PA) among older adults. However, the environmental features of these spaces and their effects on PA remain underexplored. Existing studies often overlook factors like spatial configuration, planar morphology, and bag storage facilities, and lack a systematic analytical framework. Many also rely on simplistic PA measurements and struggle with multicollinearity in data analysis. This study addresses these gaps by proposing a comprehensive framework examining four environmental dimensions: spatial configuration, planar morphology, facility provision, and visual greenery. Using GPS-tracked mobility data, behavioral audits, and multicollinearity-robust Partial Least Squares (PLS) regression, we analyze the impact of these features on PA. Results show that functional elements—higher spatial integration (VIP = 1.04), larger activity areas (VIP = 1.82), sufficient bag storage (VIP = 1.64), outdoor fitness equipment (VIP = 1.30), and diverse greenery (VIP = 1.23)—significantly enhance PA. In contrast, factors like floral diversity (VIP = 0.67), water visibility (VIP = 0.48), and shape complexity (VIP = 0.16) have minimal effects. This study provides theoretical insights and practical strategies for retrofitting paved park spaces, contributing to age-friendly urban GI.


Genomic characteristics and structural variations in the genome of P. sinensis. (a) Circos plot illustrating major genomic features of the P. sinensis genome assembly. The outermost circle comprises 34 pseudochromosomes. Features depicted from the outermost to innermost circles include (a) Copia density, (b) Gypsy density, (c) LTR retrotransposon density, (d) gene density, (e) GC content and (f) inter‐subgenome syntenic regions. All distributions are visualized within a window size of 1 Mb. (b) Structural variations between haplotypes. Comparison of structural variations between the Haplotype A (used as the reference) and Haplotype B of the P. sinensis genomes. Circles at both ends of the chromosome represent the status of telomeres, whereas solid circles indicate detected telomeres.
Phylogenetic tree constructed from conserved single‐copy synteny clusters across 12 plant species, with divergence times estimated via the PAML package. Expanded gene families are indicated in orange, and contracted families in grey. Relevant geological events (shaded in grey), 95% confidence intervals (boxed) and calibration points are annotated.
Whole‐genome duplication analysis and ancestral karyotype reconstruction of P. sinensis and Rosaceae species. (a) Categories of homologous genes across 12 Rosaceae species and BUSCO scores for each genome. (b) Distribution of synonymous substitution rates (Ks) for P. sinensis and other species within the Rosaceae family. (c) Synteny analysis of the genomes of ARK, G. trifoliata and other Maleae species. Links indicate one‐to‐one syntenic homologues between species. (d) Evolutionary trajectory from the common Rosaceae ancestor to G. trifoliata and the Maleae species.
Transcriptomic and metabolic correlation analysis in P. sinensis. (a) Distribution of different classes of metabolites identified in P. sinensis. (b) Comparison of differentially expressed metabolites (DEMs) between the S1 and S4 developmental periods in P. sinensis. (c) Relative contents of the top 10 differential expression metabolites across various stages of fruit development in P. sinensis. (d) Correlation analysis of significantly upgraded differential expression metabolites (DEMs) and modules identified through Weighted Gene Co‐expression Network Analysis (WGCNA). (e) Reconstruction of the phenylpropanoid biosynthetic pathway. Key enzyme genes involved in the rutin biosynthetic pathway include phenylpropanoid ammonium lyase (PAL), cinnamate‐4‐hydroxylase (C4H), 4‐coumarate‐CoA ligase (4CL), chalcone synthase (Teske et al., 2018), chalcone isomerase (CHI), flavanone‐3‐hydroxylase (F3H), flavonoid‐3′‐hydroxylase (F3′H), flavonol synthase (FLS), flavonoid 3‐O‐glucosyltransferase (UFGT) and flavonol‐3‐O‐glucoside L‐rhamnosyltransferase (RT). Additionally, the main enzyme genes involved in the lignin biosynthetic pathway include hydroxycinnamoyl acyltransferase (HCT), p‐coumaric acid 3‐hydroxylase (C3H), caffeoyl shikimate esterase (CSE), caffeoyl‐CoA O‐methyltransferase (CCOAMT), coumarin‐CoA reductase (CCR), cinnamyl alcohol dehydrogenase (CAD), ferulic acid 5‐hydroxylase (F5H), caffeic acid 3‐O‐methyltransferase (COMT), laccase (LAC) and peroxidase (PRX). The scaled gene expression levels (log10(TPM + 1)) at different maturation stages (S2–S4) are displayed, with gene IDs shown on the right side of each heatmap.
Overview of phenylpropanoid biosynthesis in P. sinensis. (a) Visualization of the co‐expression gene network related to key phenylpropanoid biosynthesis pathways in P. sinensis. (b) Identification of transcription factor types and quantities predicted within the yellow module of the gene network. (c) Gene expression levels of the main transcription factors involved in regulating phenylpropanoid biosynthesis. (d) Phylogenetic tree displaying the evolutionary relationships of the ODORANT (ODO1) gene in P. sinensis compared to other species. The MYBODO1 gene identified in P. sinensis is highlighted in red. (e) Representation of the key network associated with the ODORANT (ODO1) gene in P. sinensis.

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A near‐gapless genome assembly of Pseudocydonia sinensis uncovers unique phenylpropanoid pathways
  • Article
  • Full-text available

June 2025

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59 Reads

Pseudocydonia sinensis, commonly known as Chinese quince, belongs to the Rosaceae family and is closely related to apple and pear. Despite its botanical significance, genomic resources for this species remain limited. We present a high‐quality, chromosome‐scale, and haplotype‐resolved genome assembly of P. sinensis, characterized by high BUSCO completeness and QV scores. The genome sizes of Haplotypes A and B are 581.29 Mb and 561.80 Mb, respectively, each spanning 17 chromosomes with a contig N50 of 15.76 Mb. Comparative genomic analyses place P. sinensis within the Maleae tribe, closely related to Malus domestica and Pyrus communis, both of which have undergone an additional whole‐genome duplication event. Gene family and metabolomic analyses show that the genome has an expansion of 1603 gene families, with an accumulation of secondary metabolites such as flavonoids and phenolic acids (e.g. rutin and caffeoylquinic acid). This duplication has contributed to the expansion of gene families involved in secondary metabolite biosynthesis, particularly in the phenylpropanoid and flavonoid pathways. Integrative transcriptomic and metabolomic analyses further revealed the MYB transcription factor ODORANT1 (ODO1) is a key regulator of phenylpropanoid metabolism. Functional assays show that PsMYBODO1 directly binds to and activates the promoters of key genes in this pathway, including PsRT3, PsPAL, PsCAD and PsCOMT. This high‐quality reference genome provides a valuable resource for functional genomic studies and breeding programmes aimed at enhancing the medicinal properties of P. sinensis.

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MsERF17 Promotes Ethylene‐Induced Anthocyanin Biosynthesis Under Drought Conditions in Malus spectabilis Leaves

November 2024

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20 Reads

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2 Citations

Drought is an important factor that affects plant anthocyanin biosynthesis. However, the underlying molecular mechanisms remain elusive. Ethylene response factors (ERFs) are pivotal regulators in plant growth and environmental responses, particularly in anthocyanin biosynthesis. This study investigated the leaf colour transition from green to red in Malus spectabilis under drought conditions. This transition was primarily attributed to the accumulation of anthocyanins, specifically cyanidin‐3,5‐diglucoside and cyanidin‐3‐O‐galactoside. Our findings elucidate the pivotal role of MsERF17 in drought‐induced anthocyanin biosynthesis. Biochemical and molecular analyses showed that MsERF17 positively regulates anthocyanin synthesis by binding to promoters of MsbHLH3 and MsF3′ H, thereby activating their expression. Moreover, transient overexpression and virus‐induced gene silencing of MsERF17 in fruit peel and leaves, respectively, regulated anthocyanin synthesis. The stable transformation of calli further corroborated the positive regulatory function of MsERF17 in anthocyanin biosynthesis. Our results provide novel insights into the mechanism by which MsERF17, induced by ethylene, promotes anthocyanin accumulation through the positive regulation of MsbHLH3 and MsF3'H expression under drought conditions in M. spectabilis leaves.




Single-cell RNA sequencing reveals a high-resolution cell atlas of petals in Prunus mume at different flowering development stages

July 2024

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34 Reads

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2 Citations

Horticulture Research

Prunus mume (mei), a traditional ornamental plant in China, is renowned for its fragrant flowers, primarily emitted by its petals. However, the cell types of mei petals and where floral volatile synthesis occurs are rarely reported. The study used single-cell RNA sequencing to characterize the gene expression landscape in petals of P. mume ‘Fenhong Zhusha’ at budding stage (BS) and the full-blooming stage (FS). Six major cell types of petals were identified: epidermal cells (ECs), parenchyma cells (PCs), xylem parenchyma cells, phloem parenchyma cells, xylem vessels and fibers, and sieve elements and companion cells complex. Cell-specific marker genes in each cell type were provided. Floral volatiles from mei petals were measured at four flowering development stages, and their emissions increased from BS to FS, and decreased at the withering stage. Fifty-eight differentially expressed genes (DEGs) in benzenoid/phenylpropanoid pathway were screened using bulk RNA-seq data. Twenty-eight DEGs expression increased from BS to FS, indicating that they might play roles in floral volatile synthesis in P. mume, among which PmBAHD3 would participate in benzyl acetate synthesis. ScRNA-seq data showed that 27 DEGs mentioned above were expressed variously in different cell types. In situ hybridization confirmed that PmPAL2, PmCAD1, PmBAHD3,5, and PmEGS1 involved in floral volatile synthesis in mei petals are mainly expressed in EC, PC, and most vascular tissues, consistent with scRNA-seq data. The result indicates that benzyl acetate and eugenol, the characteristic volatiles in mei, are mostly synthesized in these cell types. The first petal single-cell atlas was constructed, offering new insights into the molecular mechanism of floral volatile synthesis.




The CsMYB123 and CsbHLH111 are involved in drought stress-induced anthocyanin biosynthesis in Chaenomeles speciosa

November 2023

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52 Reads

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8 Citations

Molecular Horticulture

Drought stress has been demonstrated to enhance the biosynthesis of anthocyanins in the leaves, resulting in an increased aesthetic appeal. However, the molecular mechanisms underlying drought-induced anthocyanin biosynthesis in Chaenomeles speciosa remain unclear. In this study, the metabolites of C. speciosa leaves were analyzed, and it was found that the content of cyanidin-3- O -rutinoside increased significantly under drought stress. The differentially expressed genes CsMYB123 and CsbHLH111 were isolated by transcriptomics data analysis and gene cloning, and gene overexpression and VIGS experiments verified that both play important roles in anthocyanin biosynthesis. Subsequently, Y1H and Dual-luciferase reporter assay showed that CsMYB123 binds to the promoters of anthocyanin biosynthesis-related structural genes (such as CsCHI , CsF3H , and CsANS ), while CsbHLH111 was shown to bind to the promoter of CsCHI , positively regulating its activity. Furthermore, BIFC and Y2H assays unveiled potential protein–protein interactions between CsMYB123 and CsbHLH111 at the cell nucleus. Collectively, these results shed light on the critical roles played by CsMYB123 and CsbHLH111 in anthocyanin biosynthesis, thus providing a valuable insight into understanding the molecular mechanisms of how the MYB and bHLH genes regulate anthocyanin biosynthesis in the process of leaf coloration in C. speciosa . Graphical Abstract



Citations (9)


... Infested tobacco was incubated in the dark for 1 day before being transferred to culture chambers for normal growth. The analysis for subcellular localization of DcWKY11 according to previously established methods (Xu et al. 2025;Yu et al. 2022). ...

Reference:

Combined Transcriptome and Metabolome Analysis Reveals That DcWRKY11 Promotes Methyl Jasmonate‐Induced Proanthocyanidin Biosynthesis in Dioscorea composita
MsERF17 Promotes Ethylene‐Induced Anthocyanin Biosynthesis Under Drought Conditions in Malus spectabilis Leaves

... Studies have shown that these stresses can also promote changes in the relative content of metabolites in plants. For example, under hightemperature stress, in order to absorb UV radiation and protect themselves from damage, the content of total phenols and flavonols will increase in old leaves, and drought stress can also cause some young leaves to produce more anthocyanins [15,23]. The materials of this experiment were taken from Yingde City, Guangdong Province (24 • 20 N, 113 • 21 E) in May, where the temperature is higher and the UV radiation is stronger. ...

Multi-omics analysis reveals anthocyanin synthesis is associated with drought stress tolerance in Chaenomeles speciosa flowers
  • Citing Article
  • September 2024

Journal of Cleaner Production

... They can either act independently to regulate the expression of structural genes involved in anthocyanin biosynthesis or combine to form an MBW protein complex that regulates the transcription of structural genes. Besides the aforementioned three TFs, TFs such as bZIP [6], ERF [7], SPL [8], and WRKY [9] also regulate anthocyanin biosynthesis. Additionally, recent evidence has shown that ARFs also play important roles in regulating anthocyanin biosynthesis in plants [10][11][12][13]. ...

The ERF transcription factor ZbERF3 promotes ethylene-induced anthocyanin biosynthesis in Zanthoxylum bungeanum
  • Citing Article
  • September 2024

Plant Science

... In contrast, RFF, harvested at full maturity, shows a reduction in terpenes and an increase in alcohols and ketones. These changes are closely related to metabolic transitions during fruit maturation, the regulation of metabolic pathways, and processing methods [44,45]. β-Pinene, α-pinene, sabinene, and terpinen-4-ol are the major volatile components, with relative contents exceeding 5% in both GFF and RFF samples (Table 2). ...

Widely metabolomic combined with transcriptome analysis to build a bioactive compound regulatory network for the fruit growth cycle in Pseudocydonia sinensis
  • Citing Article
  • May 2024

Food Chemistry

... And there is broad agreement that in the anthocyanin biosynthetic pathway, CHS, CHI, F3H, F3 ′ H, F3 ′ 5 ′ H (encoding flavonoid 3 ′ 5 ′ -hydroxylase, not in S. suberectus' genome), DFR, ANS, and UFGT (encoding UDPglucose flavonoid 3-O-glucosyl transferase, functioned in anthocyanidins 3-glucosylation) are critical structural genes whose expressions affect color development and alter color phenotypes [6,[24][25][26][27][28]. Additionally, MYB TFs and MBW complex were also proved to transcriptionally regulate (activate or suppress) these structural genes and, thus, had a great impact on plant color [9,[29][30][31][32][33][34]. However, in the present study, even though most of the associated crucial genes were elevated when SsMYB106 was overexpressed, no color variations (no increased/decreased anthocyanin pigmentation and other color modifications) were observed in the flowers of transiently overexpressed S. subrectus and in the flowers, leaves, and stems of stably overexpressed N. benthaminana (Figures 4 and 5). ...

The CsMYB123 and CsbHLH111 are involved in drought stress-induced anthocyanin biosynthesis in Chaenomeles speciosa

Molecular Horticulture

... While Chatzidimitriou (2016) [20] utilizes RayMan [21] for obtaining PET values after ENVI-met simulations, the majority of the authors directly obtain their comfort indexes from simulations through the Bio-Met tool, from ENVI-met [22], and validate their results using field measurements [12,16,23,24]. Additionally, recent studies have shown a growing interest in perceived human thermal comfort [25][26][27][28][29]. ...

Thermal Comfort in Urban Open Green Spaces: A Parametric Optimization Study in China's Cold Region

... Arrows represent positive regulation and blunt thick lines-negative regulation. DFR, and UFGT) and co-regulatory TF (bHLH111) = that increased the promoter-binding ability of CsMYB6 to anthocyanin structural genes [42] (Figure 3). ...

Drought‐induced CsMYB6 interacts with CsbHLH111 to regulate anthocyanin biosynthesis in Chaenomeles speciosa

... Existing scholars have conducted various types of studies to address the above issues. Zhang et al. [10] constructed a cultural heritage evaluation system; established an evaluation system through the analytic hierarchy process (AHP), the Delphi method, and fuzzy mathematics; and planned cultural and tourism routes in combination with a questionnaire survey. Hao et al. [11] assessed tourists' perception of spatial elements of three historic districts in Beijing through questionnaires and semantic analysis, used factor analysis and IPA methods to explore the influence of spatial elements on tourists' perception of the overall environment, and made suggestions for optimization. ...

Construction of cultural heritage evaluation system and personalized cultural tourism path decision model: An international historical and cultural city
  • Citing Article
  • December 2022

Journal of Urban Management

... Additionally, ZoBBX#05/06/11/12/20/21/22 /23/26/29 were predicted to interact with HY5 (ELON-GATED HYPOCOTYL 5), a TF activated by photoreceptors to promote photomorphogenesis downstream of phytochrome, cryptochrome, and UV-B photoreceptors. HY5 plays a pivotal role in photomorphogenesis and regulates various developmental processes, including seed germination, root architecture, floral organ development, fruit formation, and hormone regulation in plants [57]. Moreover, ZoBBX#01/05/10/11/29 was predicted to interact with COP1 (CONSTITUTIVELY PHOTOMOR-PHOGENIC 1), which is considered a key regulator in the suppression of photomorphogenesis [58]. ...

The UV-B-Induced Transcription Factor HY5 Regulated Anthocyanin Biosynthesis in Zanthoxylum bungeanum