Transcriptomics and Metabolomics Changes Triggered by Inflorescence Removal in Panax notoginseng (Burk.)

The root of Panax notoginseng (Burk.), in which saponins are the major active components, is a famous traditional Chinese medicine used to stop bleeding and to decrease inflammation and heart disease. Inflorescence removal increases the yield and quality of P. notoginseng, but the underlying molecular mechanisms are unknown. Here, the differences between inflorescence-removal treatment and control groups of P. notoginseng were compared using transcriptomics and metabolomics analyses. Illumina sequencing of cDNA libraries prepared from the rhizomes, leaves and roots of the two groups independently identified 6,464, 4,584, and 7,220 differentially expressed genes (DEG), respectively. In total, 345 differentially expressed transcription factors (TFs), including MYB and WRKY family members, were induced by the inflorescence-removal treatment. Additionally, 215 DEGs involved in saponin terpenoid backbone biosynthetic pathways were identified. Most genes involved in the mevalonic acid (MVA) and methylerythritol phosphate (MEP) pathways were activated by inflorescence removal. The co-expression analysis showed that the low expression levels of flavonoid biosynthesis-related genes (e.g., C4H and F3H) decreased the biosynthesis and accumulation of some flavonoids after inflorescence removal. The results not only provide new insights into the fundamental mechanisms underlying the poorly studied inflorescence-removal process in P. notoginseng and other rhizome crops, but they also represent an important resource for future research on gene functions during inflorescence-removal treatments and the reproductive stage.

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Integrated analysis of sex-biased mRNA and miRNA expression profiles in the gonad of the discus fish (Symphysodon aequifasciatus)

10.1101/492264 ◽

2018 ◽

Cited By ~ 1

Author(s):

yuanshuai Fu ◽

Zhe Xu ◽

Zaizhong Chen ◽

Bin Wen ◽

Jianzhong Gao

Keyword(s):

Molecular Mechanisms ◽

Target Genes ◽

High Efficiency ◽

Expression Profiles ◽

Gonad Development ◽

Differentially Expressed ◽

Cdna Libraries ◽

Integrated Analysis ◽

Illumina Hiseq ◽

Differentially Expressed Mirnas

The discus fish (Symphysodon aequifasciatus) is an ornamental fish that is well-known around the world. Phenotype investigation indicated that there are no significant differences in appearance between males and females of the discus fish. To better understand the sexual development mechanisms and obtain a high efficiency sex identification method in the artificial reproduction process of the discus fish, we constructed six cDNA libraries from three adult testes and three adult ovaries, and perform RNA-sequencing for identifying sex-biased candidate genes, microRNA (miRNA), and metabolic pathway using the Illumina Hiseq 4000. A total of 50,082 non-redundant genes (unigenes) were identified, of which 18,570 unigenes were significantly overexpressed in testes, and 11,182 unigenes were significantly overexpressed in ovaries, and 8 differentially expressed unigenes were validated by quantitative Real-Time PCR (qPCR). A total of 551 miRNAs were identified, of which 47 miRNAs were differentially expressed between testes and ovaries, and 7 differentially expressed miRNAs and one non-differential miRNA were validated by qPCR. Twenty-four of these differentially expressed miRNAs and their 15 predicted target genes constituted 41 important miRNA-mRNA interaction pairs, which may be important candidates for sex-related miRNAs and sex-related genes in the discus fish. Some of vital sex-related metabolic pathways were also identified that may play key roles in regulating gonad development of the discus fish. These results can provide important insights to better understand molecular mechanisms for sexual dimorphism in gonads development.

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Identification of the Genetic Basis for the Large-tailed Phenotypic Trait in Han Sheep Through Integrated mRNA and miRNA Analysis of Tail Fat Tissue Samples

10.21203/rs.3.rs-107294/v1 ◽

2020 ◽

Author(s):

Yang Guangli ◽

Zhang Huan ◽

Zhang Shuhong ◽

Li Zhiqiang ◽

Gao Fengyi ◽

...

Keyword(s):

Genetic Basis ◽

Molecular Mechanisms ◽

High Throughput Sequencing ◽

Fat Deposition ◽

Differentially Expressed ◽

Future Research ◽

Phenotypic Trait ◽

Fatty Tissue ◽

Fat Tissue ◽

Tissue Samples

Abstract Background: While evolution has led certain breeds of sheep to exhibit large tails composed of fatty tissue, the genetic basis for this fatty large-tailed phenotypic trait remains to be defined in breeds of Han sheep. Here, we employed a high-throughput sequencing approach to identify mRNAs and microRNAs (miRNAs) that were differentially expressed in tail fat tissue samples from large-tailed Han (LTH) and small-tailed Han (STH) sheep in order to identify key genetic determinants of the large-tailed phenotype.Results: In total, we identified 521 mRNAs (237 upregulated, 284 downregulated) and 14 miRNAs (6 upregulated, 8 downregulated) that were differentially expressed between these two sheep breeds. Predictive analytical database tools were subsequently utilized to identify 2,409 putative targets of these differentially expressed miRNAs (DEMs), including 65 which were among the list of differentially expressed genes (DEGs) identified in the present study. By specifically focusing on predicted DEM/DEG pairs with appropriate regulatory directionality, we identified DIRF, HSD17B12, LPL, APOBR, INSIGI, THRSP, ACSL5, FAAH, ACSS2, APOA1, ACLY, and ACSM3 through mRNA analyses and ACSL4, FTO, FGF8, IGF2, GNPDA2, LIPG, PRKAA2, ELOVL7, SOAT2, and SIRT1 through miRNA analyses as candidate genes which may regulate fat deposition and fatty acid metabolism in the adipose tissue from the tails of Han sheep. Conclusion: Together, our data provide insight into the potential genetic basis for the large-tailed phenotype of LTH sheep, suggesting that it may be attributable to specific DEMs and DEGs that regulate one another and thereby control lipid metabolism. These data provide a basis for future research regarding the role of these genes in ovine tail fat deposition, and offer preliminary perspectives on the molecular mechanisms governing the fatty large-tailed phenotype in LTH sheep.

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Advances in and prospects for Actinidia viruses

Plant Disease ◽

10.1094/pdis-10-21-2270-fe ◽

2021 ◽

Author(s):

Guoding Zhang ◽

Bixin Bai ◽

Ming Xu ◽

Yuling Liu ◽

Yunfeng Wu ◽

...

Keyword(s):

Prevention And Control ◽

Genomic Variation ◽

Future Research ◽

Fruit Crop ◽

Yield And Quality ◽

Actinidia Spp ◽

And Control ◽

Propagation Material

Kiwifruit (Actinidia spp.) is an economically important fruit crop worldwide. Before 2010, kiwifruit viruses had not received much attention; since then, more than 20 viruses infecting kiwifruit have been discovered. Some of these viruses cause severe yellowing, mosaic, necrosis, ringspots and other symptoms on leaves, seriously impacting yield and quality. Many of these viruses are widely distributed. This review summarizes recent research advances in the identification, genomic variation, distribution, transmission, detection, incidence, prevention and control of kiwifruit viruses and proposes directions for future research. Using virus-tested propagation material is the most economical and effective method for controlling kiwifruit viruses.

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Activity and Function Studies of The Promoter Cis-Acting Elements of The Key Enzymes in Saponins Biosynthesis of DS From Panax Notoginseng

10.21203/rs.3.rs-136213/v1 ◽

2020 ◽

Author(s):

Yujie Zheng ◽

Rongyu Shao ◽

Pengguo Xia ◽

Zongsuo Liang ◽

Kaijing Yan

Keyword(s):

Gene Expression ◽

Gene Expression Regulation ◽

Panax Notoginseng ◽

Promoter Sequence ◽

Upstream Region ◽

Future Research ◽

Active Components ◽

Cis Acting ◽

Plant Expression Vector ◽

Important Region

Abstract Background：Panax notoginseng is a traditional Chinese medicine for the treatment of blood diseases, in which saponins were the main active components. Dammarenediol synthase (DS) is a key enzyme in the saponin synthesis pathway of P. notoginseng.The promoter is an important region to regulate gene expression, and the study of the promoter sequence provides important evidence for revealing the mechanism of gene expression regulation. Methods: However, there was still little research on the promoter function of P. notoginseng. In this study, the 1382 bp promoter upstream of DS from P. notoginseng was cloned and sequenced. The promoter sequence was analyzed by online databases. The plant expression vector fused with the β-glucuronidase gene was constructed, transferred into Agrobacterium tumefaciens. Then tobacco was injected, and its response to exogenous hormones (gibberellin and abscisic acid) was studied by transient expression to verify its unique action elements. Results: The results showed that the tobacco leaves transferred with DS promoter had significantly increased GUS protease activity after spraying GA and ABA, indicating that both DS promoter can specifically and significantly respond to exogenous GA and ABA signal. Conclusions: These findings will help us to better understand the regulatory mechanisms of the upstream region of the DS gene and provide a basis for future research on the interaction of cis-acting elements of promoters with related transcription factors.

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Comparative transcriptomic analysis reveals key components controlling spathe color in Anthurium andraeanum (Hort.)

PLoS ONE ◽

10.1371/journal.pone.0261364 ◽

2021 ◽

Vol 16 (12) ◽

pp. e0261364

Author(s):

Jaime A. Osorio-Guarín ◽

David Gopaulchan ◽

Corey Quanckenbush ◽

Adrian M. Lennon ◽

Pathmanathan Umaharan ◽

...

Keyword(s):

Developmental Stages ◽

De Novo ◽

Genetic Model ◽

Differentially Expressed ◽

Cdna Libraries ◽

Future Research ◽

Sequence Information ◽

Anthocyanin Pathway ◽

Late Developmental Stage ◽

Anthurium Andraeanum

Anthurium andraeanum (Hort.) is an important ornamental in the tropical cut-flower industry. However, there is currently insufficient information to establish a clear connection between the genetic model(s) proposed and the putative genes involved in the differentiation between colors. In this study, 18 cDNA libraries related to the spathe color and developmental stages of A. andraeanum were characterized by transcriptome sequencing (RNA-seq). For the de novo transcriptome, a total of 114,334,082 primary sequence reads were obtained from the Illumina sequencer and were assembled into 151,652 unigenes. Approximately 58,476 transcripts were generated and used for comparative transcriptome analysis between three cultivars that differ in spathe color (‘Sasha’ (white), ‘Honduras’ (red), and ‘Rapido’ (purple)). A large number of differentially expressed genes (8,324), potentially involved in multiple biological and metabolic pathways, were identified, including genes in the flavonoid and anthocyanin biosynthetic pathways. Our results showed that the chalcone isomerase (CHI) gene presented the strongest evidence for an association with differences in color and the highest correlation with other key genes (flavanone 3-hydroxylase (F3H), flavonoid 3’5’ hydroxylase (F3’5’H)/ flavonoid 3’-hydroxylase (F3’H), and leucoanthocyanidin dioxygenase (LDOX)) in the anthocyanin pathway. We also identified a differentially expressed cytochrome P450 gene in the late developmental stage of the purple spathe that appeared to determine the difference between the red- and purple-colored spathes. Furthermore, transcription factors related to putative MYB-domain protein that may control anthocyanin pathway were identified through a weighted gene co-expression network analysis (WGCNA). The results provided basic sequence information for future research on spathe color, which have important implications for this ornamental breeding strategies.

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Comparative transcriptomic analysis reveals key components controlling spathe color in Anthurium andraeanum (Hort.)

10.1101/2020.12.29.424726 ◽

2020 ◽

Author(s):

Jaime A. Osorio-Guarín ◽

David Gopaulchan ◽

Corey Quackenbush ◽

Adrian M. Lennon ◽

Pathmanathan Umaharan ◽

...

Keyword(s):

Developmental Stage ◽

Biosynthetic Pathway ◽

Differentially Expressed ◽

Cdna Libraries ◽

Future Research ◽

Sequence Information ◽

List Type ◽

Domain Protein ◽

Anthurium Andraeanum ◽

Myb Domain

ABSTRACTAnthurium andraeanum (Hort.) is an important ornamental in the tropical cut-flower industry. However, there is currently not enough information to establish a clear connection between the genetic model(s) proposed and the putative genes involved in the differentiation between colors. In this study, 18 cDNA libraries related to the spathe color and developmental stages of A. andraeanum cut-flowers were characterized by transcriptome sequencing technology. For the de novo transcriptome, a total of 114,334,082 primary sequence reads were obtained from the Illumina sequencer and were assembled into 151,652 unigenes. Approximately 58,476 transcripts were generated and used for comparative transcriptome analysis between three varieties that differ in spathe color (‘Sasha’ (white), ‘Honduras’ (red), and ‘Rapido’ (purple)). A large number of differentially expressed genes (8,324) that were potentially involved in multiple biological and metabolic pathways were identified, including the flavonoid and anthocyanin biosynthetic pathways. Our results showed that chalcone synthase (CHS) and flavonoid 3’-hydroxylase (F3’H) were the main genes differentially expressed in the white/red/purple comparison. We also identified a differentially expressed cytochrome P450 in the late developmental stage of the purple spathe that appeared to determine the difference between the red- and purple-colored spathes. Additionally, putative MYB-domain protein candidates that could be responsible for the control of the biosynthetic pathway were identified. The results provided basic sequence information for future research on spathe color, which have important implications for breeding strategies in this ornamental.Core ideasRNA-seq was performed on three anthurium varieties.Gene expression was compared for developmental stage and spathe color.Differentially expressed unigenes were identified.Putative MYB-domain protein candidates of the anthocyanin biosynthetic pathway were identified.

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Transcriptomic analyses reveal putative genes associated with bibenzyl biosynthesis in the traditional Chinese herb Dendrobium officinale

10.21203/rs.2.17392/v1 ◽

2019 ◽

Author(s):

Oluwaniyi Isaiah Adejobi ◽

Ju Guan ◽

Liu Yang ◽

Jiang-Miao Hu ◽

Anmin Yu ◽

...

Keyword(s):

Secondary Metabolites ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Chinese Herb ◽

Differentially Expressed ◽

Experimental Result ◽

Dendrobium Officinale ◽

Future Research ◽

Traditional Chinese Herbal Medicine ◽

Root Tissues

Abstract Background: Dendrobium plants are well known for their uses in traditional Chinese herbal medicine. Bibenzyl compounds are the main active compounds in Dendrobium officinale. However, the physiological and molecular basis for the biosynthesis of bibenzyl compounds in Dendrobium plants remains underexplored. Results: In this study, the accumulation of erianin and gigantol were studied as representative compounds of bibenzyl. Their presence in plant tissues were investigated. Our results show that root tissues contained the highest content of bibenzyl (erianin and gigantol). Based on the pre-experimental result that exogenous application of Methyl-Jasmonate promotes the biosynthesis of bibenzyl compounds in D. officinale root tissues, comparative transcriptomic analyses were conducted between the bibenzyl-accumulated root tissues and a control. In total, we identified 1,342 differentially expressed genes (DEGs) with 912 up-regulated and 430 down-regulated genes. Most of the identified DEGs are functionally involved in the JA signaling pathway and the biosynthesis of secondary metabolites. In particular, we identified 11 enzymatic genes functionally involved in bibenzyl biosynthesis.Conclusions: Our study provide insights on the identification of putative genes associated with bibenzyl biosynthesis and accumulation in Dendrobium plants, and also paves the way for future research on dissecting the physiological and molecular mechanisms of bibenzyl synthesis in plants as well as on how to best utilize genetic engineering and molecular modification techniques to genetically improve Dendrobium varieties by increasing the content of bibenzyl for drug production and industrialization. Keywords: Bibenzyl, D. officinale , Differentially expressed genes, Secondary metabolites, Transcriptome analysis.

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Transcriptomic Analyses of the Hypothalamic-Pituitary-Gonadal Axis Identify Candidate Genes Related to Egg Production in Xinjiang Yili Geese

Animals ◽

10.3390/ani10010090 ◽

2020 ◽

Vol 10 (1) ◽

pp. 90

Author(s):

Yingping Wu ◽

Xiaoyu Zhao ◽

Li Chen ◽

Junhua Wang ◽

Yuqing Duan ◽

...

Keyword(s):

Candidate Genes ◽

Differentially Expressed Genes ◽

Egg Production ◽

Molecular Mechanisms ◽

Egg Laying ◽

Differentially Expressed ◽

Cdna Libraries ◽

Receptor Interaction ◽

Sequencing Data ◽

Pituitary Glands

The study was conducted to investigate the transcriptomic differences of the hypothalamic-pituitary-gonadal axis between Xinjiang Yili geese with high and low egg production and to find candidate genes regulating the egg production of Xinjiang Yili geese. The 8 selected Xinjiang Yili Geese with high or low egg production (4 for each group) were 3 years old, with good health, and under the same feeding condition. High-throughput sequencing technology was used to sequence cDNA libraries of the hypothalami, pituitary glands, and ovaries. The sequencing data were compared and analyzed, and the transcripts with significant differences were identified and analyzed with bioinformatics. The study showed that the transcriptome sequencing data of the 24 samples contained a total of 1,176,496,146 valid reads and 176.47 gigabase data. Differential expression analyses identified 135, 56, and 331 genes in the hypothalami, pituitary glands, and ovaries of Xinjiang Yili geese with high and low egg production. Further annotation of these differentially expressed genes in the non-redundant protein sequence database (Nr) revealed that 98, 52, and 309 genes were annotated, respectively. Through the annotations of GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) databases, 30 candidate genes related to the egg production of Xinjiang Yili geese were preliminarily selected. The gap junction, focal adhesion, and ECM-receptor interaction signaling pathways were enriched with the hypothalamic, pituitary, and ovarian differentially expressed genes, and the calcium signaling pathway was enriched with the pituitary and ovarian differentially expressed genes. Thus, these pathways in the hypothalamic-pituitary-gonadal axis may play an important role in regulating egg production of Xinjiang Yili geese. The results provided the transcriptomic information of the hypothalamic-pituitary-gonadal axis of Xinjiang Yili geese and laid the theoretical basis for revealing the molecular mechanisms regulating the egg-laying traits of Xinjiang Yili geese.

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Congenital cystic adenomatoid malformations of the lung: an epithelial transcriptomic approach

Respiratory Research ◽

10.1186/s12931-020-1306-5 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Guillaume Lezmi ◽

Shamila Vibhushan ◽

Claudia Bevilaqua ◽

Nicolas Crapart ◽

Nicolas Cagnard ◽

...

Keyword(s):

Molecular Mechanisms ◽

Branching Morphogenesis ◽

Transcriptomic Analysis ◽

Differentially Expressed ◽

Protein Levels ◽

Redundant Genes ◽

And Control ◽

Laser Capture ◽

Congenital Cystic Adenomatoid Malformations

Abstract Background The pathophysiology of congenital cystic adenomatoid malformations (CCAM) of the lung remains poorly understood. Aim This study aimed to identify more precisely the molecular mechanisms limited to a compartment of lung tissue, through a transcriptomic analysis of the epithelium of macrocystic forms. Methods Tissue fragments displaying CCAM were obtained during planned surgical resections. Epithelial mRNA was obtained from cystic and normal areas after laser capture microdissection (LCM). Transcriptomic analyses were performed and the results were confirmed by RT-PCR and immunohistochemistry in independent samples. Results After controlling for RNA quality, we analysed the transcriptomes of six cystic areas and five control areas. In total, 393 transcripts were differentially expressed in the epithelium, between CCAM and control areas. The most highly redundant genes involved in biological functions and signalling pathways differentially expressed between CCAM and control epithelium included TGFB2, TGFBR1, and MAP 2 K1. These genes were considered particularly relevant as they have been implicated in branching morphogenesis. RT-qPCR analysis confirmed in independent samples that TGFBR1 was more strongly expressed in CCAM than in control tissues (p < 0.03). Immunohistochemistry analysis showed TGFBR1 (p = 0.0007) and TGFB2 (p < 0.02) levels to be significantly higher in the epithelium of CCAM than in that of control tissues. Conclusions This compartmentalised transcriptomic analysis of the epithelium of macrocystic lung malformations identified a dysregulation of TGFB signalling at the mRNA and protein levels, suggesting a possible role of this pathway in CCAM pathogenesis. Trial registration ClinicalTrials.gov Identifier: NCT01732185.

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Microarray gene expression profiles in dilated and hypertrophic cardiomyopathic end-stage heart failure

Physiological Genomics ◽

10.1152/physiolgenomics.00122.2001 ◽

2002 ◽

Vol 10 (1) ◽

pp. 31-44 ◽

Cited By ~ 168

Author(s):

Juey-Jen Hwang ◽

Paul D. Allen ◽

George C. Tseng ◽

Ching-Wan Lam ◽

Lameh Fananapazir ◽

...

Keyword(s):

Heart Failure ◽

Cdna Microarray ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Statistical Significance ◽

Left Ventricular ◽

Differentially Expressed ◽

Cdna Libraries ◽

Microarray Technology ◽

Microarray Gene Expression

Despite similar clinical endpoints, heart failure resulting from dilated cardiomyopathy (DCM) or hypertrophic cardiomyopathy (HCM) appears to develop through different remodeling and molecular pathways. Current understanding of heart failure has been facilitated by microarray technology. We constructed an in-house spotted cDNA microarray using 10,272 unique clones from various cardiovascular cDNA libraries sequenced and annotated in our laboratory. RNA samples were obtained from left ventricular tissues of precardiac transplantation DCM and HCM patients and were hybridized against normal adult heart reference RNA. After filtering, differentially expressed genes were determined using novel analyzing software. We demonstrated that normalization for cDNA microarray data is slide-dependent and nonlinear. The feasibility of this model was validated by quantitative real-time reverse transcription-PCR, and the accuracy rate depended on the fold change and statistical significance level. Our results showed that 192 genes were highly expressed in both DCM and HCM (e.g., atrial natriuretic peptide, CD59, decorin, elongation factor 2, and heat shock protein 90), and 51 genes were downregulated in both conditions (e.g., elastin, sarcoplasmic/endoplasmic reticulum Ca2+-ATPase). We also identified several genes differentially expressed between DCM and HCM (e.g., αB-crystallin, antagonizer of myc transcriptional activity, β-dystrobrevin, calsequestrin, lipocortin, and lumican). Microarray technology provides us with a genomic approach to explore the genetic markers and molecular mechanisms leading to heart failure.

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