Exploring regulatory network of icariin synthesis in Herba Epimedii through integrated omics analysis.

Herba Epimedii's leaves are highly valued in traditional Chinese medicine for their substantial concentration of flavonoids, which play a crucial role in manifesting the plant's therapeutic properties. This study investigated the metabolomic, transcriptomic and proteomic profiles of leaves from two Herba Epimedii cultivars, Epipremnum sagittatum (J) and Epipremnum pubescens (R), at three different developmental stages. Metabolite identification and analysis revealed a total of 1,412 and 1,421 metabolites with known structures were found. Flavonoids made up of 33%, including 10 significant accumulated icariin analogues. Transcriptomic analysis unveiled totally 41,644 differentially expressed genes (DEGs) containing five encoded genes participated in icariin biosynthesis pathways. Totally, 9,745 differentially expressed proteins (DEPs) were found, including Cluster-47248.2.p1 (UDP-glucuronosy/UDP-glucosyltransferase), Cluster-30441.2.p1 (O-glucosyltransferase), and Cluster-28344.9.p1 (anthocyanidin 3-O-glucoside 2 "-O-glucosyltransferase-like) through proteomics analysis which are involved to icariin biosynthesis. Protein-protein interaction (PPI) assay exhibited, totally 12 proteins showing a strong relationship of false discovery rate (FDR) <0.05 with these three proteins containing 2 leucine-rich repeat receptor kinase-like protein SRF7, and 5 methyl jasmonate esterase 1. Multi-omics connection networks uncovered 237 DEGs and 72 DEPs exhibited significant associations with the 10 icariin analogues. Overall, our integrated omics approach provides comprehensive insights into the regulatory network underlying icariin synthesis in Herba Epimedii, offering valuable resources for further research and development in medicinal plant cultivation and pharmaceutical applications.

Manufacturing agglomeration, urban form, and haze pollution.

Manufacturing agglomeration promotes rapid economic development while also causing severe environmental pollution. This paper investigates the impact and mechanism of manufacturing agglomeration on haze pollution from the Chinese city level. Furthermore, we discuss the moderating effect and threshold effect of the three urban forms of urban external shape complexity, urban compactness, and urban fragmentation on the relationship between the two. The result shows the following: (1) The aggregation of the manufacturing industry presents an inverted U-shaped characteristic of promoting first and then inhibiting haze pollution in China's overall, eastern and central regions. (2) The complexity of the city's external shape and the city's fragmentation has a positive moderating effect on the relationship between manufacturing agglomeration and haze pollution. And urban fragmentation shows a negative moderating effect on the relationship between the two when the level of manufacturing agglomeration is on the right side of the inverted U-shaped curve. (3) The urban form shows a significant double threshold characteristic for haze pollution, increasing the complexity of the city's external shape and the city's fragmentation. The agglomeration of manufacturing shows the characteristics of first inhibiting and then promoting haze pollution. As urban compactness increases, the inhibitory effect of manufacturing agglomeration on haze pollution increases.

Transcriptomic and Weighted Gene Co-expression Correlation Network Analysis Reveal Resveratrol Biosynthesis Mechanisms Caused by Bud Sport in Grape Berry.

Resveratrol is a natural polyphenol compound produced in response to biotic and abiotic stresses in grape berries. However, changes in resveratrol caused by bud sport in grapes are scarcely reported. In this study, trans-resveratrol and cis-resveratrol were identified and quantified in the grape berries of 'Summer Black' and its bud sport 'Nantaihutezao' from the veraison to ripening stages using ultra performance liquid chromatography-high resolution tandem mass spectrometry (UPLC-HRMS). We found that bud sport accumulates the trans-resveratrol earlier and increases the contents of cis-resveratrol in the earlier stages but decreases its contents in the later stages. Simultaneously, we used RNA-Seq to identify 51 transcripts involved in the stilbene pathways. In particular, we further identified 124 and 19 transcripts that negatively correlated with the contents of trans-resveratrol and cis-resveratrol, respectively, and four transcripts encoding F3'5'H that positively correlated with the contents of trans-resveratrol by weighted gene co-expression network analysis (WGCNA). These transcripts may play important roles in relation to the synergistic regulation of metabolisms of resveratrol. The results of this study can provide a theoretical basis for the genetic improvement of grapes.

Can Industrial Collaborative Agglomeration Reduce Haze Pollution? City-Level Empirical Evidence from China.

We analyze the mechanism for industrial co-agglomeration in Chinese 283 cities to affect haze pollution from 2003 to 2016 and examine the possible mediating effects of urbanization and energy structure between haze pollution and industrial co-agglomeration, finally obtaining the following results. First, industrial co-agglomeration and haze pollution across China, including central and eastern regions keep a typical inverted U-shaped curve relationship. That is, industrial co-agglomeration first promotes haze pollution and then restrains it. However, the impact of industrial co-agglomeration on haze pollution in western China is still on the left side of the inverted U-shaped curve, reflecting a promotion effect. Second, industrial co-agglomeration has a significant spatial spillover effect on haze pollution. Additionally, industrial co-agglomeration can promote haze pollution in local regions but inhibit it in surrounding regions in both the short and long run. In contrast, when the industrial co-agglomeration index exceeds the inflection point (3.6531), it benefits the reduction of haze pollution in local regions, while not being conducive to it in the neighboring regions. Third, industrial co-agglomeration can affect haze pollution through urbanization and energy structure, that is, urbanization and energy structure play an intermediary role between them.

Comparative transcriptomic analysis between 'Summer Black' and its bud sport 'Nantaihutezao' during developmental stages.

MAIN CONCLUSION: 4-coumarate-CoA ligase (VIT_02s0109g00250) and copper amine oxidase (VIT_17s0000g09100) played essential roles in contributing to the total soluble solid and total anthocyanin variations induced by bud sport in grape berries. Taste and color, which are important organoleptic qualities of grape berry, undergo rapid and substantial changes during development and ripening. In this study, we used two cultivars 'Summer Black' and its bud sport 'Nantaihutezao' to explore and identify differentially expressed genes associated with total soluble solid and anthocyanin during developmental stages using RNA-Seq. Overall, substantial differences in expression were observed across berry development between the two cultivars. 5388 genes were detected by weighted gene co-expression network analysis (WGCNA) associated with the total soluble solid (TSS) and anthocyanin contents variations. Several of these genes were significantly enriched in the phenylalanine metabolism pathway; two hub genes 4-coumarate-CoA ligase (VIT_02s0109g00250) and copper amine oxidase (VIT_17s0000g09100) played the most essential roles in relating to the total soluble solid and total anthocyanin variations induced by bud sport through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and co-expression network analysis. These findings provide insights into the molecular mechanism responsible for the bud sport phenotype.

Erratum: Publisher Correction: Cytological, physiological, and transcriptomic analyses of golden leaf coloration in Ginkgo biloba L.

[This corrects the article DOI: 10.1038/s41438-018-0015-4.].

Cytological, physiological, and transcriptomic analyses of golden leaf coloration in Ginkgo biloba L.

Ginkgo biloba is grown worldwide as an ornamental plant for its golden leaf color. However, the regulatory mechanism of leaf coloration in G. biloba remains unclear. Here, we compared G. biloba gold-colored mutant leaves and normal green leaves in cytological, physiological and transcriptomic terms. We found that chloroplasts of the mutant were fewer and smaller, and exhibited ruptured thylakoid membranes, indistinct stromal lamellae and irregularly arranged vesicles. Physiological experiments also showed that the mutant had a lower chlorophyll, lower flavonoid and higher carotenoid contents (especially lutein). We further used transcriptomic sequencing to identify 116 differentially expressed genes (DEGs) and 46 transcription factors (TFs) involved in chloroplast development, chlorophyll metabolism, pigment biosynthesis and photosynthesis. Among these, the chlorophyll biosynthesis-related PPO showed down-regulation, while chlorophyll degradation-related NYC/NOL had up-regulated expression in mutant leaves. Z-ISO, ZDS, and LCYE, which are involved in carotenoid biosynthesis were up-regulated. Quantitative real-time PCR (RT-qPCR) further confirmed the altered expression levels of these genes at three stages. The alteration of PPO and NYC/NOL gene expression might affect chlorophyll biosynthesis and promote degradation of chlorophyll b to chlorophyll a, while the up-regulated genes Z-ISO, ZDS and LCYE enhanced carotenoid accumulation. Consequently, changes in the ratio of carotenoids to chlorophylls were the main factors driving the golden leaf coloration in the mutant G. biloba.