Metabolomic and Transcriptomic Analysis of the Anthocyanin Regulatory Networks in Malus Domestica Borkh. Peel with Different Color Patterns

2021 ◽  
Author(s):  
Pengwei Duan ◽  
Xiaojian Ma ◽  
Lizhe Qin ◽  
Jizhuang Du ◽  
Guoliang Xu ◽  
...  
Keyword(s):  
Malus Domestica ◽  
Regulatory Networks ◽  
Anthocyanin Biosynthesis ◽  
Differentially Expressed ◽  
Color Patterns ◽  
Bhlh Genes ◽  
Apple Peel ◽  
Fuji Apple ◽  
Different Color ◽  
Apple Peels

Abstract Background:Coloring is an important external quality of ‘Fuji’ apple (Malus domestica Borkh.) and there are two color patterns of apple peels, i.e., stripe and blush. The objectives of this study were to reveal the anthocyanin biosynthesis metabolic pathway in striped and blushed peels of Malus domestica using metabolomics and transcriptomics, to identify different anthocyanin metabolites, and to analyze the differentially expressed genes involved in anthocyanin biosynthesis.Result:The metabolite concentration and gene expression were profiled in the striped and blushed fruit peels of apple harvested at three ripening periods to elucidate the color formation mechanism. At the green fruit period, there were 83 DAMs,including 30 flavonoids, 674 DEGs (521 up-regulated and 153 down-regulated),including 3 MYB related genes (up-regulated, LOC103415449, LOC103421948, LOC103432338) and 2 bHLH genes(up-regulated, LOC103436250, LOC103437863) between striped and blushed apple.At the color turning period, there were 48 DAMs,including 20 flavonoids, 880 DEGs (274 up-regulated and 606 down-regulated), including 3 differentially expressed E2.3.1.133, HCT genes(down-regulated), 2 differentially expressed F3H genes (down-regulated), 1 differentially expressed BZ1 gene (down-regulated) and 2 differentially expressed ANS genes (up-regulated) and 2 up-regulated MYB related genes (LOC103411576, LOC103412495), 5 down-regulated MYB related genes(LOC103400953, LOC103408672, LOC103415404, LOC103420697, LOC103421948), 1 differentially expressed bHLH gene(down-regulated, LOC103400870). At the complete coloring period，there were 95 DAMs,including 34 flavonoids, 2258 DEGs (1159 up- and 1099 down-regulated), including 3 differentially expressed E2.3.1.133, HCT genes(down-regulated), 1 differentially expressed E2.3.1.133, HCT genes(up-regulated), 2 differentially expressed CYP98A genes (up-regulated), 4 differentially expressed CHS genes (up-regulated), 2 differentially expressed E5.5.1.6 genes(up-regulated), 2 differentially expressed CYP75B1 genes (up-regulated), 2 differentially expressed F3R genes (up-regulated), 2 differentially expressed ANS genes (up-regulated), 1 differentially expressed DFR genes (up-regulated), 2 differentially expressed BZ1 genes (up-regulated) and 1 differentially expressed MYB related gene (up-regulated, LOC103401575) .There were both 10 kinds of cyanidin in apple peel at color turning period and complete coloring period, Keracyanin and Cyanin were up-regulated at color turning period and Cyanidin-3-O-(6''-O-malonyl)glucoside was up-regulated at complete coloring period.Conclusions: Our researches provide important information on the anthocyanin metabolites and the candidate genes involved in the anthocyanin biosynthesis pathways of Fuji apple in M.domestcia.

scholarly journals Nighttime Temperatures and Sunlight Intensities Interact to Influence Anthocyanin Biosynthesis and Photooxidative Sunburn in “Fuji” Apple

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaomin Xue ◽  
Ying Duan ◽  
Jinzheng Wang ◽  
Fengwang Ma ◽  
Pengmin Li
Keyword(s):  
Light Intensity ◽  
Low Temperatures ◽  
Anthocyanin Biosynthesis ◽  
High Light ◽  
Anthocyanin Accumulation ◽  
Low Light ◽  
Low Light Intensity ◽  
Apple Peel ◽  
Fuji Apple ◽  
Nighttime Temperatures

Light and low temperatures induce anthocyanin accumulation, but intense sunlight causes photooxidative sunburn. Nonetheless, there have been few studies of anthocyanin synthesis under different sunlight intensities and low nighttime temperatures. Here, low nighttime temperatures followed by low light intensity were associated with greater anthocyanin accumulation and the expression of anthocyanin biosynthesis genes in “Fuji” apple peel. UDP-glucose flavonoid-3-O-glucosyltransferase (UFGT) activity was positively associated with anthocyanin enrichment. Ascorbic acid can be used as an electron donor of APX to scavenge H2O2 in plants, which makes it play an important role in oxidative defense. Exogenous ascorbate altered the anthocyanin accumulation and reduced the occurrence of high light–induced photooxidative sunburn by removing hydrogen peroxide from the peel. Overall, low light intensity was beneficial for the accumulation of anthocyanin and did not cause photooxidative sunburn, whereas natural light had the opposite effect on the apple peel at low nighttime temperatures. This study provides an insight into the mechanisms by which low temperatures induce apple coloration and high light intensity causes photooxidative sunburn.

scholarly journals Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in Salvia miltiorrhiza Bge. flowers

2020 ◽  
Author(s):  
Tao Jiang ◽  
Meide Zhang ◽  
Chunxiu Wen ◽  
Xiaoliang Xie ◽  
Wei Tian ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Regulatory Networks ◽  
Anthocyanin Biosynthesis ◽  
Salvia Miltiorrhiza ◽  
Flower Color ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Anthocyanin Content ◽  
Transcriptomics Data

Abstract Background: The study objectives were to reveal the anthocyanin biosynthesis metabolic pathway in white and purple flowers of Salvia miltiorrhiza using metabolomics and transcriptomics, to identify different anthocyanin metabolites, and to analyze the differentially expressed genes involved in anthocyanin biosynthesis . Results: We analyzed the metabolomics and transcriptomics data of Salvia miltiorrhiza flowers. A total of 1994 differentially expressed genes and 84 flavonoid metabolites were identified between the white and purple flowers of Salvia miltiorrhiza . Integrated analysis of transcriptomic and metabolomics showed that cyanidin 3,5-O-diglucoside, malvidin 3,5-diglucoside, and cyanidin 3-O-galactoside were mainly responsible for the purple flower color of Salvia miltiorrhiza. A total of 100 unigenes encoding 10 enzymes were identified as candidate genes involved in anthocyanin biosynthesis in Salvia miltiorrhiza flowers. The low expression of the ANS gene decreased the anthocyanin content but enhanced the accumulation of flavonoids in Salvia miltiorrhiza flowers. Conclusions: Our results provide valuable information on the anthocyanin metabolites and the candidate genes involved in the anthocyanin biosynthesis pathways in Salvia miltiorrhiza .

Differential protective effects of polyphenol extracts from apple peels and fleshes against acute CCl4-induced liver damage in mice

2015 ◽  
Vol 6 (2) ◽  
pp. 513-524 ◽  
Author(s):  
Yan Nie ◽  
Daoyuan Ren ◽  
Xinshan Lu ◽  
Yanfei Sun ◽  
Xingbin Yang
Keyword(s):  
Liver Damage ◽  
Hepatic Damage ◽  
Protective Effects ◽  
Polyphenolic Extract ◽  
Apple Peel ◽  
Phenolic Profiles ◽  
Fuji Apple ◽  
Apple Peels

The present study reports the phenolic profiles and antioxidant and hepatoprotective properties of Red Fuji apple peel polyphenolic extract (APP) and its flesh polyphenolic extract (AFP) against CCl4-induced acute hepatic damage in mice.

scholarly journals apterous A specifies dorsal wing patterns and sexual traits in butterflies

2017 ◽  
Author(s):  
Anupama Prakash ◽  
Antónia Monteiro
Keyword(s):  
Transcription Factor ◽  
Regulatory Networks ◽  
Sexually Dimorphic ◽  
Color Patterns ◽  
Bicyclus Anynana ◽  
Sexual Ornaments ◽  
Wing Patterns ◽  
Specific Factors ◽  
Different Color

AbstractButterflies have evolved different color patterns on their dorsal and ventral wing surfaces to serve different signaling functions, yet the developmental mechanisms controlling surface-specific patterning are still unknown. Here, we mutate both copies of the transcription factor apterous in Bicyclus anynana butterflies using CRISPR/Cas9 and show that apterous A functions both as a repressor and modifier of ventral wing color patterns, as well as a promoter of dorsal sexual ornaments in males. We propose that the surface-specific diversification of wing patterns in butterflies proceeded via the co-option of apterous A into various gene regulatory networks involved in the differentiation of discrete wing traits. Further, interactions between apterous and sex-specific factors such as doublesex may have contributed to the origin of sexually dimorphic surface-specific patterns. Finally, we discuss the evolution of eyespot pattern diversity in the family Nymphalidae within the context of developmental constraints due to apterous regulation.Significance statementButterflies have evolved different wing patterns on their dorsal and ventral wing surfaces that serve different signaling functions. We identify the transcription factor, apterous A, as a key regulator of this surface-specific differentiation in butterflies. We also show a role for apterous A in restricting the developmental origin of a novel trait, eyespots, to just the ventral wing surface. Dorsal-ventral differentiation of tissues is not just restricted to butterfly wings but occurs in many other organs and organisms from arthropods to humans. Thus, we believe that our work will be of interest to a diverse group of biologists and layman alike interested in the role of development in shaping biodiversity.

Genome-Wide Identification of differently expressed lncRNAs, mRNAs, and circRNAs in patients with osteoarthritis

2020 ◽  
Vol 15 ◽  
Author(s):  
Yeqing Sun ◽  
Lei Chen ◽  
Yingqi Zhang ◽  
Jincheng Zhang ◽  
Shashi Ranjan Tiwari
Keyword(s):  
Regulatory Networks ◽  
Expression Profiles ◽  
Interleukin 1 ◽  
Interaction Network ◽  
Circular Rna ◽  
Negative Regulation ◽  
Differentially Expressed ◽  
Positive Regulation ◽  
Proteinprotein Interaction ◽  
Differently Expressed Genes

Background: Osteoarthritis (OA), one of the most important causes leading to joint disability, was considered as an untreatable disease. A series of genes were reported to regulate the pathogenesis of OA, including microRNAs, Long non-coding RNAs and Circular RNA. So far, the expression profiles and functions of lncRNAs, mRNAs, and circRNAs in OA are not fully understood. Objective: The present study aimed to identify differently expressed genes in OA. Methods: The present study conducted RNA-seq to identify differently expressed genes in OA. Ontology (GO) analysis was used to analysis the Molecular Function and Biological Process. KEGG pathway analysis was used to perform the differentially expressed lncRNAs in biological pathways. Results: Hierarchical clustering revealed a total of 943 mRNAs, 518 lncRNAs, and 300 circRNAs were dysregulated in OA compared to normal samples. Furthermore, we constructed differentially expressed mRNAs mediated proteinprotein interaction network, differentially expressed lncRNAs mediated trans regulatory networks, and competitive endogenous RNA (ceRNA) to reveal the interaction among these genes in OA. Bioinformatics analysis revealed these dysregulated genes were involved in regulating multiple biological processes, such as wound healing, negative regulation of ossification, sister chromatid cohesion, positive regulation of interleukin-1 alpha production, sodium ion transmembrane transport, positive regulation of cell migration, and negative regulation of inflammatory response. To the best of our knowledge, this study for the first time revealed the expression pattern of mRNAs, lncRNAs and circRNAs in OA. Conclusion: This study provided novel information to validate these differentially expressed RNAs may be as possible biomarkers and targets in OA.

Estimating the copy number of the agouti signaling protein (ASIP) gene in goat breeds with different color patterns

2021 ◽  
Vol 246 ◽  
pp. 104440
Author(s):  
Dailu Guan ◽  
Anna Castelló ◽  
María Gracia Luigi-Sierra ◽  
Vincenzo Landi ◽  
Juan Vicente Delgado ◽  
...  
Keyword(s):  
Copy Number ◽  
Color Patterns ◽  
Signaling Protein ◽  
Different Color

scholarly journals Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jifang Zhang ◽  
Jian Zhao ◽  
Qunyun Tan ◽  
Xiaojun Qiu ◽  
Shiyong Mei
Keyword(s):  
Transcription Factors ◽  
Raphanus Sativus ◽  
Regulatory Networks ◽  
Anthocyanin Biosynthesis ◽  
Comparative Transcriptome ◽  
Structural Genes ◽  
Key Genes ◽  
Transcript Profiles ◽  
Species Specific ◽  
Anthocyanin Biosynthetic Genes

AbstractRadish (Raphanus sativus) is an important vegetable worldwide that exhibits different flesh and skin colors. The anthocyanins responsible for the red and purple coloring in radishes possess nutritional value and pharmaceutical potential. To explore the structural and regulatory networks related to anthocyanin biosynthesis and identify key genes, we performed comparative transcriptome analyses of the skin and flesh of six colored radish accessions. The transcript profiles showed that each accession had a species-specific transcript profile. For radish pigmentation accumulation, the expression levels of anthocyanin biosynthetic genes (RsTT4, RsC4H, RsTT7, RsCCOAMT, RsDFR, and RsLDOX) were significantly upregulated in the red- and purple-colored accessions, but were downregulated or absent in the white and black accessions. The correlation test, combined with metabolome (PCC > 0.95), revealed five structural genes (RsTT4, RsDFR, RsCCOAMT, RsF3H, and RsBG8L) and three transcription factors (RsTT8-1, RsTT8-2, and RsPAR1) to be significantly correlated with flavonoids in the skin of the taproot. Four structural genes (RsBG8L, RsDFR, RsCCOAMT, and RsLDOX) and nine transcription factors (RsTT8-1, RsTT8-2, RsMYB24L, RsbHLH57, RsPAR2L, RsbHLH113L, RsOGR3L, RsMYB24, and RsMYB34L) were found to be significantly correlated with metabolites in the flesh of the taproot. This study provides a foundation for future studies on the gene functions and genetic diversity of radish pigmentation and should aid in the cultivation of new valuable radish varieties.

Hydrothermal Synthesis of Carbon Dots from Luochuan Red Fuji Apple Peel and Application for the Detection of Fe3+ Ions

NANO ◽  
2021 ◽  
Author(s):  
Shun-Sheng Zhao ◽  
Yakun Wang ◽  
Zaiwen Yang ◽  
Xiangrong Liu ◽  
Zheng Yang ◽  
...  
Keyword(s):  
Hydrothermal Synthesis ◽  
Carbon Dots ◽  
Apple Peel ◽  
Fuji Apple

scholarly journals Ultrabithorax Is a Micromanager of Hindwing Identity in Butterflies and Moths

2021 ◽  
Vol 9 ◽  
Author(s):  
Amruta Tendolkar ◽  
Aaron F. Pomerantz ◽  
Christa Heryanto ◽  
Paul D. Shirk ◽  
Nipam H. Patel ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Targeted Mutagenesis ◽  
Junonia Coenia ◽  
Wing Venation ◽  
Loss Of Function ◽  
Color Patterns ◽  
Wide Range ◽  
Range Of Functions ◽  
Gene Regulatory ◽  
Pyralid Moth

The forewings and hindwings of butterflies and moths (Lepidoptera) are differentiated from each other, with segment-specific morphologies and color patterns that mediate a wide range of functions in flight, signaling, and protection. The Hox gene Ultrabithorax (Ubx) is a master selector gene that differentiates metathoracic from mesothoracic identities across winged insects, and previous work has shown this role extends to at least some of the color patterns from the butterfly hindwing. Here we used CRISPR targeted mutagenesis to generate Ubx loss-of-function somatic mutations in two nymphalid butterflies (Junonia coenia, Vanessa cardui) and a pyralid moth (Plodia interpunctella). The resulting mosaic clones yielded hindwing-to-forewing transformations, showing Ubx is necessary for specifying many aspects of hindwing-specific identities, including scale morphologies, color patterns, and wing venation and structure. These homeotic phenotypes showed cell-autonomous, sharp transitions between mutant and non-mutant scales, except for clones that encroached into the border ocelli (eyespots) and resulted in composite and non-autonomous effects on eyespot ring determination. In the pyralid moth, homeotic clones converted the folding and depigmented hindwing into rigid and pigmented composites, affected the wing-coupling frenulum, and induced ectopic scent-scales in male androconia. These data confirm Ubx is a master selector of lepidopteran hindwing identity and suggest it acts on many gene regulatory networks involved in wing development and patterning.

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