scholarly journals Metabolome and transcriptome profiling provide insights into green apple peel reveals light- and UV-B-responsive pathway in anthocyanins accumulation

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ruirui Ding ◽  
Xingkai Che ◽  
Zhen Shen ◽  
Yuanhu Zhang
Keyword(s):  
Transcription Factors ◽  
Visible Light ◽  
Candidate Genes ◽  
Metabolic Flux ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Ultraviolet B ◽  
Pcr Analysis ◽  
Apple Variety ◽  
Qrt Pcr

Abstract Background In nature, green apple are associated with the accumulation of chlorophyll, while red apple varieties are associated with anthocyanins accumulation. Notably, in this study, the green skin color apple variety ‘white winter pearmain’ treated with ultraviolet-B (UV-B) exhibited red skins and marked anthocyanin accumulation, while visible light could not. But there are few reports on the biosynthesis difference of anthocyanins in green apple by visible light and UV-B-treatment. Here, we explored the difference of metabolites and genes expression level in green apple by transcriptomic and metabolic. Results The metabolic analysis revealed that there were 152 and 178 significantly changed metabolites in the visible light and UV-B-treated green apple, respectively, compared to the control, and flavone, flavonol, and anthocyanin were the most significantly increased; and transcriptomic analysis showed that 37,110 and 37,709 differentially expressed genes, including 382 and 475 transcription factors (TFs) were detected in light and UV-B-treatment fruit, respectively. Quantitative reverse transcription PCR (qRT-PCR) results confirmed changes in the expression levels of genes encoding metabolites involved in the flavonoid synthesis pathways. The flavonoid metabolic flux in the UV-B treatment increased the accumulation of cyanidin 3-glucoside and cyanidin 3, 5-diglucoside compared to under the light-treatment. Furthermore, we performed qRT-PCR analysis of anthocyanin biosynthesis genes and predicted the gene of MD00G1134400 (a UDP glucose-flavonoid 3–0-glucosyltransferase) may be a candidate gene for anthocyanins accumulation and highly expressed in UV-B-treatment fruit. Expression profiles of several transcription factors of the families MYB, bHLH, NAC were highly correlated with the content of the anthocyanin. Conclusions The composition and contents of anthocyanins in green apple in UV-B-treatment very greatly. A series of metabolites and candidate genes were revealed through combined analysis of metabolome and transcriptome. These results provide an important data for dissecting candidate genes and molecular basis governing green apple color formation in response to visible light and UV-B light.

scholarly journals Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion

2019 ◽  
Author(s):  
Huanhuan Liu ◽  
Jikai Ma ◽  
Huogen Li
Keyword(s):  
Candidate Genes ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Periodic Acid ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Nectar Secretion ◽  
Relict Species ◽  
Periodic Acid Schiff ◽  
Real Time Quantitative Pcr

Abstract Background Nectar is a major flower attractant and reward for insects for pollination. Liriodendron, a genus of the Magnoliaceae family, has only two relict species, L. chinense and L. tulipifera, that are considered “basal angiosperms” according to plant evolutionary history. The flowers of Liriodendron plants are insect pollinated and secrete nectar to attract pollinators. To date, the morphology and anatomy of the nectary, the mechanism of nectar secretion and the molecular mechanism involved in nectary development in Liriodendron remain poorly understood. Methods In this study, we examined the nectary surface cells and the change in starch in L. tulipifera by using scanning electron microscopy and periodic acid-Schiff techniques to select definitive samples for next research. Transcriptome sequencing was performed on the top and middle parts of the immature nectary and the middle parts of the mature nectary and the postsecreted nectary in L. tulipifera. We evaluated the expression profiles of 22 DEGs that were closely related to nectary development and nectar secretion for real-time quantitative PCR analysis. Results The L. tulipifera nectary is a starch-storing nectary and is located in the top and middle parts of L. tulipifera petals. After analyzing the RNA-seq data, we obtained 115.26 Gb clean data in 12 libraries and mapped the results to the L. chinense reference genome with 71.02%-79.77% efficiency. In total, 26,955 DEGs were identified by analyzing six different pairwise comparisons. The flavonoid biosynthesis, phenylpropanoid biosynthesis, anthocyanin biosynthesis and starch and sucrose metabolism pathways were enriched and related to nectar secretion and pigment change. We identified 56 transcription factor families, and members of the TCP, Trihelix, C2H2, ERF, and MADS families changed dynamically during nectary development. Moreover, to further verify the accuracy of the RNA-seq results, we validated the expression profiles of 22 candidate genes. Conclusions We evaluated the nectary development and secretion process comprehensively and identified many related candidate genes in L. tulipifera. These findings suggest that the nectary may play important roles in flavonoid synthesis and petal color presentation.

scholarly journals Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion

2019 ◽  
Author(s):  
Huanhuan Liu ◽  
Jikai Ma ◽  
Huogen Li
Keyword(s):  
Candidate Genes ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Periodic Acid ◽  
Middle Part ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Nectar Secretion ◽  
Relict Species ◽  
Periodic Acid Schiff

Abstract Background: Nectar is a major floral attractant and reward for insects that ensures pollination. Liriodendron, a genus of the Magnoliaceae family, includes only two relict species, L. chinense and L. tulipifera, which are considered “basal angiosperms” according to plant evolutionary history. The flowers of Liriodendron plants are insect pollinated and secrete nectar to attract pollinators. To date, the morphology and anatomy of nectaries, the mechanism of nectar secretion and the molecular mechanism of nectary development in Liriodendron remain poorly understood. Methods: In this study, we examined the nectary surface cells and change in starch in L. tulipifera by using scanning electron microscopy and periodic acid-Schiff techniques to select appropriate samples for subsequent research. Transcriptome sequencing was of the top and middle parts of immature nectaries and the middle part of mature and postsecretory nectaries in L. tulipifera was performed. We evaluated the expression profiles of 21 DEGs that are closely related to nectary development and nectar secretion for real-time quantitative PCR analysis. Results: L. tulipifera nectaries are starch-storing nectaries and are located in the top and middle parts of L. tulipifera petals. After analyzing the RNA-seq data, we obtained 115.26 Gb of clean data in 12 libraries and mapped the results to the L. chinense reference genome with 71.02%-79.77% efficiency. In total, 26,955 DEGs were identified by performing six pairwise comparisons. The flavonoid biosynthesis, phenylpropanoid biosynthesis, anthocyanin biosynthesis and starch and sucrose metabolism pathways were enriched and related to nectar secretion and pigment change. We identified 56 transcription factor families, and members of the TCP, Trihelix, C2H2, ERF, and MADS families changed dynamically during nectary development. Moreover, to further verify the accuracy of the RNA-seq results, we validated the expression profiles of 21 candidate genes. Conclusions: We evaluated the nectary development and secretion processes comprehensively and identified many related candidate genes in L. tulipifera. These findings suggest that nectaries play important roles in flavonoid synthesis and petal color presentation.

scholarly journals Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Huanhuan Liu ◽  
Jikai Ma ◽  
Huogen Li
Keyword(s):  
Candidate Genes ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Periodic Acid ◽  
Middle Part ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Nectar Secretion ◽  
Relict Species ◽  
Periodic Acid Schiff

Abstract Background Nectar is a major floral attractant and reward for insects that ensures pollination. Liriodendron, a genus of the Magnoliaceae family, includes only two relict species, L. chinense and L. tulipifera, which are considered “basal angiosperms” according to plant evolutionary history. The flowers of Liriodendron plants are insect pollinated and secrete nectar to attract pollinators. To date, the morphology and anatomy of nectaries, the mechanism of nectar secretion and the molecular mechanism of nectary development in Liriodendron remain poorly understood. Methods In this study, we examined the nectary surface cells and change in starch in L. tulipifera by using scanning electron microscopy and periodic acid-Schiff techniques to select appropriate samples for subsequent research. Transcriptome sequencing was of the top and middle parts of immature nectaries and the middle part of mature and postsecretory nectaries in L. tulipifera was performed. We evaluated the expression profiles of 21 DEGs that are closely related to nectary development and nectar secretion for real-time quantitative PCR analysis. Results L. tulipifera nectaries are starch-storing nectaries and are located in the top and middle parts of L. tulipifera petals. After analyzing the RNA-seq data, we obtained 115.26 Gb of clean data in 12 libraries and mapped the results to the L. chinense reference genome with 71.02–79.77% efficiency. In total, 26,955 DEGs were identified by performing six pairwise comparisons. The flavonoid biosynthesis, phenylpropanoid biosynthesis, anthocyanin biosynthesis and starch and sucrose metabolism pathways were enriched and related to nectar secretion and pigment change. We identified 56 transcription factor families, and members of the TCP, Trihelix, C2H2, ERF, and MADS families changed dynamically during nectary development. Moreover, to further verify the accuracy of the RNA-seq results, we validated the expression profiles of 21 candidate genes. Conclusions We evaluated the nectary development and secretion processes comprehensively and identified many related candidate genes in L. tulipifera. These findings suggest that nectaries play important roles in flavonoid synthesis and petal color presentation.

Molecular analysis of anthocyanin biosynthesis-related genes reveal BoTT8 associated with purple hypocotyl of broccoli (Brassica oleracea var. italica L.)

Genome ◽  
2019 ◽  
Vol 62 (4) ◽  
pp. 253-266 ◽  
Author(s):  
Md Abdur Rahim ◽  
Khandker Shazia Afrin ◽  
Hee-Jeong Jung ◽  
Hoy-Taek Kim ◽  
Jong-In Park ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Environmental Factors ◽  
Brassica Oleracea ◽  
Candidate Genes ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Market Value ◽  
Breeding Programs ◽  
Qrt Pcr ◽  
Early Seedling

Broccoli (Brassica oleracea var. italica L.) is a highly nutritious vegetable that typically forms pure green or purple florets. However, green broccoli florets sometimes accumulate slight purplish pigmentation in response environmental factors, decreasing their market value. In the present study, we aimed to develop molecular markers to distinguish broccoli genotypes as pure green or purplish floret color at the early seedling stage. Anthocyanins are known to be involved in the purple pigmentation in plants. The purplish broccoli lines were shown to accumulate purple pigmentation in the hypocotyls of very young seedlings; therefore, the expression profiles of the structural and regulatory genes of anthocyanin biosynthesis were analyzed in the hypocotyls using qRT-PCR. BoPAL, BoDFR, BoMYB114, BoTT8, BoMYC1.1, BoMYC1.2, and BoTTG1 were identified as putative candidate genes responsible for the purple hypocotyl color. BoTT8 was much more highly expressed in the purple than green hypocotyls; therefore, it was cloned and sequenced from various broccoli lines, revealing SNP and InDel variations between these genotypes. We tested four SNPs (G > A; A > T; G > C; T > G) in the first three exons and a 14-bp InDel (ATATTTATATATAT) in the BoTT8 promoter in 51 broccoli genotypes, and we found these genetic variations could distinguish the green lines, purple lines, and F1 hybrids. These novel molecular markers could be useful in broccoli breeding programs to develop a true green or purple broccoli cultivar.

scholarly journals Transcriptomic and microstructural analyses in Liriodendron tulipifera Linn. reveal candidate genes involved in nectary development and nectar secretion

2019 ◽  
Author(s):  
Huanhuan Liu ◽  
Jikai Ma ◽  
Huogen Li
Keyword(s):  
Candidate Genes ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Periodic Acid ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Nectar Secretion ◽  
Relict Species ◽  
Periodic Acid Schiff ◽  
Real Time Quantitative Pcr

Abstract Background Nectar is a major flower attractant and reward for insects for pollination. Liriodendron , a genus of the Magnoliaceae family, has only two relict species, L. chinense and L. tulipifera , that are considered “basal angiosperms” according to plant evolutionary history. The flowers of Liriodendron plants are insect pollinated and secrete nectar to attract pollinators. To date, the morphology and anatomy of the nectary, the mechanism of nectar secretion and the molecular mechanism involved in nectary development in Liriodendron remain poorly understood. Methods In this study, we examined the nectary surface cells and the change in starch in L. tulipifera by using scanning electron microscopy and periodic acid-Schiff techniques to select definitive samples for next research. Transcriptome sequencing was performed on the top and middle parts of the immature nectary and the middle parts of the mature nectary and the postsecreted nectary in L. tulipifera . We evaluated the expression profiles of 21 DEGs that were closely related to nectary development and nectar secretion for real-time quantitative PCR analysis. Results The L. tulipifera nectary is a starch-storing nectary and is located in the top and middle parts of L . tulipifera petals. After analyzing the RNA-seq data, we obtained 115.26 Gb clean data in 12 libraries and mapped the results to the L. chinense reference genome with 71.02%-79.77% efficiency. In total, 26,955 DEGs were identified by analyzing six different pairwise comparisons. The flavonoid biosynthesis, phenylpropanoid biosynthesis, anthocyanin biosynthesis and starch and sucrose metabolism pathways were enriched and related to nectar secretion and pigment change. We identified 56 transcription factor families, and members of the TCP, Trihelix, C2H2, ERF, and MADS families changed dynamically during nectary development. Moreover, to further verify the accuracy of the RNA-seq results, we validated the expression profiles of 21 candidate genes. Conclusions We evaluated the nectary development and secretion process comprehensively and identified many related candidate genes in L. tulipifera . These findings suggest that the nectary may play important roles in flavonoid synthesis and petal color presentation.

Dysregulation of tRNA-derived small RNAs and their potential roles in lupus nephritis

Lupus ◽  
2021 ◽  
pp. 096120332110614
Author(s):  
Yan Liang ◽  
Ji Zhang ◽  
Wenxian Qiu ◽  
Bo Chen ◽  
Ying Zhou ◽  
...  
Keyword(s):  
Lupus Nephritis ◽  
Signaling Pathway ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Mapk Signaling ◽  
Pcr Analysis ◽  
Clinical Indicators ◽  
Qrt Pcr

Objective Lupus nephritis (LN) is a major end-organ complication of systemic lupus erythematosus (SLE), and the molecular mechanism of LN is not completely clear. Accumulating pieces of evidence indicate the potential vital role of tRNA-derived small RNAs (tsRNAs) in human diseases. Current study aimed to investigate the potential roles of tsRNAs in LN. Methods We herein employed high‐throughput sequencing to screen the expression profiles of tsRNAs in renal tissues of the LN and control groups. To validate the sequencing data, we performed quantitative real-time PCR (qRT-PCR) analysis. Correlational analysis of verified tsRNAs expression and clinical indicators was conducted using linear regression. The potential target genes were also predicted. The biological functions of tsRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Results Our findings revealed that the expression profiles of tsRNAs were significantly altered in the kidney tissues from LN patients compared with control. Overall, 160 tsRNAs were significantly dysregulated in the LN group, of which 79 were upregulated, whereas 81 were downregulated. Subsequent qRT-PCR results confirmed the different expression of candidate tsRNAs. Correlation analysis results found that expression of verified tsRNAs were correlated to clinical indicators. The target prediction results revealed that verified tsRNAs might act on 712 target genes. Further bioinformatics analysis uncovered tsRNAs might participate in the pathogenesis of LN through several associated pathways, including cell adhesion molecules, MAPK signaling pathway, PI3K-Akt signaling pathway and B cell receptor signaling pathway. Conclusion This study provides a novel insight for studying the mechanism of LN.

scholarly journals Effects of Certain cis-Regulatory Elements on Stage-Specific vitellogenin Expression in the Bombyx mori (Lepidoptera: Bombycidae)

2020 ◽  
Vol 20 (3) ◽  
Author(s):  
Guanwang Shen ◽  
Hongling Liu ◽  
Ying Lin ◽  
Dongxu Xing ◽  
Yujing Zhang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Transcription Factors ◽  
Bombyx Mori ◽  
Regulatory Network ◽  
Theoretical Basis ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Qrt Pcr ◽  
Stage Specificity ◽  
E Box

Abstract Bombyx mori vitellogenin (BmVg) is highly upregulated during pupation, and the 20-hydroxyecdysone and amino acids may regulate stage-specific BmVg expression. However, previous studies showed that other factors may also affect stage-specific BmVg expression. Here, we characterized effective BmVg transcription factors by identifying the corresponding cis-regulatory elements (CREs). We prepared transgenic B. mori, in which DsRed was driven by various lengths of BmVg promoter. qRT-PCR analysis showed that DsRed expression driven by a 1.0-kb BmVg promoter (VgP1.0K) was consistent with endogenous BmVg. VgP1.0K specificity was closer to the endogenous BmVg promoter than that of VgP0.8K. These results suggest that CREs affecting stage-specific BmVg expression were localized to the 1.0-kb BmVg promoter. We investigated the effects of certain CREs that could influence the stage specificity of BmVg promoter on BmVg expression in transgenic B. mori. The relative DsRed expression was significantly reduced in transgenic female B. mori and the peak in DsRed expression was delayed after E-box CRE mutation. These results demonstrate that the E-box element enhanced BmVg expression and also affected stage-specific BmVg expression. Moreover, the relative DsRed expression was significantly increased in transgenic female of B. mori after 3×BD CRE mutation in BmVg promoter. However, the stage specificity of the mutated promoter was consistent with that of the endogenous BmVg promoter. The 3×BD element downregulated BmVg but had no effect on stage-specific BmVg expression. The present study promoted the process of elucidating the regulatory network for stage-specific BmVg expression and furnished a theoretical basis for the application of BmVg promoter.

scholarly journals Comparison of Stemness and Gene Expression between Gingiva and Dental Follicles in Children

2016 ◽  
Vol 2016 ◽  
pp. 1-11 ◽  
Author(s):  
Chung-Min Kang ◽  
Seong-Oh Kim ◽  
Mijeong Jeon ◽  
Hyung-Jun Choi ◽  
Han-Sung Jung ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cells ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Pcr Analysis ◽  
Expression Levels ◽  
Qrt Pcr ◽  
Stem Cell Source ◽  
Regenerative Dentistry ◽  
Induced Pluripotent

The aim of this study was to compare the differential gene expression and stemness in the human gingiva and dental follicles (DFs) according to their biological characteristics. Gingiva (n=9) and DFs (n=9) were collected from 18 children. Comparative gene expression profiles were collected using cDNA microarray. The expression of development, chemotaxis, mesenchymal stem cells (MSCs), and induced pluripotent stem cells (iPSs) related genes was assessed by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Histological analysis was performed using hematoxylin-eosin and immunohistochemical staining. Gingiva had greater expression of genes related to keratinization, ectodermal development, and chemotaxis whereas DFs exhibited higher expression levels of genes related to tooth and embryo development. qRT-PCR analysis showed that the expression levels of iPSc factors includingSOX2,KLF4, andC-MYCwere58.5±26.3,12.4±3.5, and12.2±1.9times higher in gingiva andVCAM1(CD146) andALCAM(CD166) were33.5±6.9and4.3±0.8times higher in DFs. Genes related to MSCs markers includingCD13,CD34,CD73,CD90, andCD105were expressed at higher levels in DFs. The results of qRT-PCR and IHC staining supported the microarray analysis results. Interestingly, this study demonstrated transcription factors of iPS cells were expressed at higher levels in the gingiva. Given the minimal surgical discomfort and simple accessibility, gingiva is a good candidate stem cell source in regenerative dentistry.

scholarly journals Genome-Wide Identification and Characterization of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Red Walnut (Juglans regia L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Wei Zhao ◽  
Yonghui Liu ◽  
Lin Li ◽  
Haijun Meng ◽  
Ying Yang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Family ◽  
Developmental Stage ◽  
Molecular Mechanisms ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Juglans Regia ◽  
Expression Patterns ◽  
Regulatory Elements

Basic helix-loop-helix (bHLH) proteins are transcription factors (TFs) that have been shown to regulate anthocyanin biosynthesis in many plant species. However, the bHLH gene family in walnut (Juglans regia L.) has not yet been reported. In this study, 102 bHLH genes were identified in the walnut genome and were classified into 15 subfamilies according to sequence similarity and phylogenetic relationships. The gene structure, conserved domains, and chromosome location of the genes were analyzed by bioinformatic methods. Gene duplication analyses revealed that 42 JrbHLHs were involved in the expansion of the walnut bHLH gene family. We also characterized cis-regulatory elements of these genes and performed Gene Ontology enrichment analysis of gene functions, and examined protein-protein interactions. Four candidate genes (JrEGL1a, JrEGL1b, JrbHLHA1, and JrbHLHA2) were found to have high homology to genes encoding bHLH TFs involved in anthocyanin biosynthesis in other plants. RNA sequencing revealed tissue- and developmental stage-specific expression profiles and distinct expression patterns of JrbHLHs according to phenotype (red vs. green leaves) and developmental stage in red walnut hybrid progeny, which were confirmed by quantitative real-time PCR analysis. All four of the candidate JrbHLH proteins localized to the nucleus, consistent with a TF function. These results provide a basis for the functional characterization of bHLH genes and investigations on the molecular mechanisms of anthocyanin biosynthesis in red walnut.

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