scholarly journals Analysis of miRNA-mediated Regulation of Flowering Induction in Lilium × formolongi

2020 ◽  
Author(s):  
Qian Zhang ◽  
Yu-Qian Zhao ◽  
Xue Gao ◽  
Guixia Jia
Keyword(s):  
Vegetative Growth ◽  
Carbon Fixation ◽  
Expression Profiles ◽  
Growth Period ◽  
Pentose Phosphate ◽  
Differentially Expressed ◽  
Vegetative Development ◽  
Flowering Induction ◽  
Flowering Initiation ◽  
Pathway Analyses

Abstract Background: MicroRNAs play pivotal roles in plant vegetative phase change and flowering induction via integrating into multiple flowering pathways. Lilium × formolongi is an important ornamental lily cultivar that can flower within one year after sowing. However, it remains unresolved how miRNA-mediated regulation networks contribute to the L. × formolongi characteristics of a short vegetative growth period and rapid flowering.Results: In this study, five small RNA libraries and one degradome library were constructed for L. × formolongi during vegetative growth and flowering initiation, and 366 conserved miRNAs and 32 novel miRNAs were identified. Additionally, 84 miRNAs were significantly differentially expressed during development. A total of 396 targets of 185 miRNAs were identified and validated through degradome sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that functions of the targets were top enriched in the cold and cadmium ion responses, pentose phosphate pathway and carbon fixation in photosynthetic organisms pathway. Furthermore, among 23 differentially expressed miRNA-target pairs, the miR156s-LfSPL2, miR172a-LfAP2 and miR164a-LfNAC pairs as well as miR159a-LfSPL2 were found to be relevant to flowering based on the correlation analysis of expression profiles in the miRNA libraries, degradome and transcriptome. A coexpression regulatory network focused on differentially expressed pairs was also constructed by WGCNA, and 14 miRNAs were considered putative key miRNAs during vegetative development and flowering induction. miR156a/ d/ e showed particularly strong relationships with other miRNAs in the coexpression network. Conclusions: This study provides cues for the further exploration of the regulatory mechanisms of short vegetative development and flowering in L. × formolongi.

scholarly journals Analysis of miRNA-mediated regulation of flowering induction in Lilium × formolongi

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Qian Zhang ◽  
Yu-Qian Zhao ◽  
Xue Gao ◽  
Gui-Xia Jia
Keyword(s):  
Vegetative Growth ◽  
Carbon Fixation ◽  
Expression Profiles ◽  
Growth Period ◽  
Pentose Phosphate ◽  
Differentially Expressed ◽  
Vegetative Development ◽  
Flowering Induction ◽  
Flowering Initiation ◽  
Pathway Analyses

Abstract Background MicroRNAs play pivotal roles in plant vegetative phase change and flowering induction via integrating into multiple flowering pathways. Lilium × formolongi is an important ornamental lily cultivar that can flower within one year after sowing. However, it remains unresolved how miRNA-mediated regulation networks contribute to the L. × formolongi characteristics of a short vegetative growth period and rapid flowering. Results In this study, the small RNA libraries and one degradome library were constructed for L. × formolongi during vegetative growth and flowering initiation, and 366 conserved miRNAs and 32 novel miRNAs were identified. Additionally, 84 miRNAs were significantly differentially expressed during development. A total of 396 targets of 185 miRNAs were identified and validated through degradome sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that functions of the targets were top enriched in the cold and cadmium ion responses, pentose phosphate pathway and carbon fixation in photosynthetic organisms. Furthermore, among 23 differentially expressed miRNA-target pairs, the miR156s-LfSPL2, miR172a-LfAP2 and miR164a-LfNAC pairs as well as miR159a-LfSPL2 were found to be relevant to flowering based on the correlation analysis of expression profiles in the miRNA libraries, degradome and transcriptome. A coexpression regulatory network focused on differentially expressed pairs was also constructed by WGCNA, and 14 miRNAs were considered putative key miRNAs during vegetative development and flowering induction. miR156a/ d/ e showed particularly strong relationships with other miRNAs in the coexpression network. Conclusions This study provides cues for the further exploration of the regulatory mechanisms of short vegetative development and flowering in L. × formolongi.

scholarly journals Transcriptome profiling of peanut (Arachis hypogaea) gynophores in gravitropic response

2013 ◽  
Vol 40 (12) ◽  
pp. 1249 ◽  
Author(s):  
Hai-fen Li ◽  
Xiao-Ping Chen ◽  
Fang-he Zhu ◽  
Hai-Yan Liu ◽  
Yan-Bin Hong ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Arachis Hypogaea ◽  
Molecular Mechanisms ◽  
Carbon Fixation ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Pentose Phosphate ◽  
Differentially Expressed ◽  
Pcr Analysis

Peanut (Arachis hypogaea L.) produces flowers aerially, but the fruit develops underground. This process is mediated by the gynophore, which always grows vertically downwards. The genetic basis underlying gravitropic bending of gynophores is not well understood. To identify genes related to gynophore gravitropism, gene expression profiles of gynophores cultured in vitro with tip pointing upward (gravitropic stimulation sample) and downward (control) at both 6 and 12 h were compared through a high-density peanut microarray. After gravitropic stimulation, there were 174 differentially expressed genes, including 91 upregulated and 83 downregulated genes at 6 h, and 491 differentially expressed genes including 129 upregulated and 362 downregulated genes at 12 h. The differentially expressed genes identified were assigned to 24 functional categories. Twenty pathways including carbon fixation, aminoacyl-tRNA biosynthesis, pentose phosphate pathway, starch and sucrose metabolism were identified. The quantitative real-time PCR analysis was performed for validation of microarray results. Our study paves the way to better understand the molecular mechanisms underlying the peanut gynophore gravitropism.

Response of soya beans to planting date in south-eastern Queensland. II.* Vegetative and reproductive development

1974 ◽  
Vol 25 (5) ◽  
pp. 723 ◽  
Author(s):  
RJ Lawn ◽  
DE Byth
Keyword(s):  
Seed Yield ◽  
Vegetative Growth ◽  
Growth Period ◽  
Reproductive Development ◽  
Planting Date ◽  
Biological Efficiency ◽  
Vegetative Development ◽  
Planting Dates ◽  
Growing Period ◽  
Seed Yields

Vegetative and reproductive development of a range of soya bean cultivars was studied over a series of planting dates in both hill plots and row culture at Redland Bay, Qld. Responses in the extent of vegetative and reproductive development were related to changes in the phasic developmental patterns. The duration and extent of vegetative development for the various cultivar-planting date combinations were closely associated with the length of the period from planting to the cessation of flowering. Thus, vegetative growth was greatest for those planting dates which resulted in a delay in flowering and/or extended the flowering phase. Similarly, genetic lateness of maturity among cultivars was associated with more extensive vegetative development. Seed yield per unit area increased within each cultivar as the length of the growing period was extended until sufficient vegetative growth occurred to allow the formation of closed canopies under the particular agronomic conditions imposed. Further increases in the length of the period of vegetative growth failed to increase seed yield, and in some cases seed yields were actually reduced. Biological efficiency of seed production (BE) was negatively correlated with the length of the vegetative growth period. Differences in BE among cultivar-planting date combinations were large. It is suggested that maximization of seed yield will necessitate an optimum compromise between the degree of vegetative development and BE. Optimum plant arrangement will therefore vary, depending on the particular cultivar-planting date combination. ___________________ \*Part I, Aust. J. Agric. Res., 24: 67 (1973).

scholarly journals Microarray profile of B cells from Graves’ disease patients reveals biomarkers of proliferation

2020 ◽  
Vol 9 (5) ◽  
pp. 405-417
Author(s):  
Xuechao Jiang ◽  
Yonghui Wang ◽  
Xiaoying Li ◽  
Leqi He ◽  
Qian Yang ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
B Cells ◽  
B Cell ◽  
Expression Profiles ◽  
Interaction Network ◽  
Thyroid Stimulating Hormone ◽  
Sh2 Domain ◽  
Differentially Expressed ◽  
Graves Disease ◽  
Pathway Analyses

B lymphocytes are the source of autoantibodies against the thyroid-stimulating hormone receptor (TSHR) in Graves’ disease (GD). Characterization of autoimmune B-cell expression profiles might enable a better understanding of GD pathogenesis. To reveal this, the expression levels of long noncoding RNAs (lncRNAs) and mRNAs (genes) in purified B cells from patients with newly diagnosed GD and healthy individuals were compared using microarrays, which elucidated 604 differentially expressed lncRNAs (DE-lncRNAs) and 410 differentially expressed genes (DEGs). GO and pathway analyses revealed that the DEGs are mainly involved in immune response. A protein–protein interaction network presented experimentally validated interactions among the DEGs. Two independent algorithms were used to identify the DE-lncRNAs that regulate the DEGs. Functional annotation of the deregulated lncRNA–mRNA pairs identified 14 pairs with mRNAs involved in cell proliferation. The lncRNAs TCONS_00022357-XLOC_010919 and n335641 were predicted to regulate TCL1 family AKT coactivator A (TCL1A), and the lncRNA n337845 was predicted to regulate SH2 domain containing 1A (SH2D1A). TCL1A and SH2D1A are highly involved in B-cell proliferation. The differential expression of both genes was validated by qRT-PCR. In conclusion, lncRNA and mRNA expression profiles of B cells from patients with GD indicated that the lncRNA–mRNA pairs n335641–TCL1A, TCONS_00022357-XLOC_010919–TCL1A, and n337845–SH2D1A may participate in GD pathogenesis by modulating B-cell proliferation and survival. Therefore, the identified lncRNA and mRNA may represent novel biomarkers and therapeutic targets for GD.

scholarly journals Changes of miRNA Expression Profiles from Cervical-Vaginal Fluid-Derived Exosomes in Response to HPV16 Infection

2020 ◽  
Vol 2020 ◽  
pp. 1-8
Author(s):  
Ying Wu ◽  
Xinyan Wang ◽  
Li Meng ◽  
Wenqu Li ◽  
Chunyan Li ◽  
...  
Keyword(s):  
Cervical Cancer ◽  
Signaling Pathway ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Differentially Expressed ◽  
Vaginal Fluid ◽  
Exosomal Mirnas ◽  
Differentially Expressed Mirnas ◽  
Pathway Analyses ◽  
Hpv16 Infection

As an oncogenic virus, HPV16 can lead to the dysfunction of cervical epithelial cells and contribute to the progression of cervical cancer. Components from the cervical-vaginal fluid (CVF) could be used as the basis for cervical cancer screening. Exosomes are widely present in various body fluids and participate in intercellular communication via its cargos of proteins, mRNAs, and miRNAs. This study was conducted to explore the changes of miRNAs in exosomes isolated form the cervical-vaginal fluid during HPV16 infection and to predict the potential effects of exosomal miRNAs on the development of cervical cancer. CVF was collected from volunteers with or without HPV16 infection. The exosomes in CVF were identified by electron microscopy. Microarray analysis was subjected to find the differentially expressed miRNAs in CVF exosomes. To confirm the results, 16 miRNAs were randomly selected to go through real-time quantitative polymerase chain reaction. In addition, GO and pathway analyses were conducted to reveal potential functions of differentially expressed miRNAs. A total of 2548 conserved miRNAs were identified in the cervical-vaginal fluid-derived exosomes. In response to HPV16 infection, 45 miRNAs are significantly upregulated and 55 miRNAs are significantly downregulated (P<0.05). The GO and KEGG pathway analyses revealed that these differentially expressed miRNAs are tightly associated with cervical cancer tumorigenesis, through interaction with the Notch signaling pathway, TNF signaling pathway, and TGF-β signaling pathway. These results suggest that exosomal miRNAs in CVF are differentially expressed in HPV16 infection patients and HPV16-free volunteers. It provided a novel insight to understand the underlying mechanism of HPV16 infection in regulating cervical cancer progression.

scholarly journals Identification of Novel LncRNA Biomarkers and Construction of LncRNA-Related Networks in Han Chinese Patients with Ischemic Stroke

2018 ◽  
Vol 50 (6) ◽  
pp. 2157-2175 ◽  
Author(s):  
Xiaojing Guo ◽  
Jialei Yang ◽  
Baoyun Liang ◽  
Tingting Shen ◽  
Yan Yan ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Regulatory Network ◽  
Human Peripheral Blood ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Chinese Patients ◽  
Cerebral Disease ◽  
Significant Differential Expression ◽  
Qrt Pcr ◽  
Pathway Analyses

Background/Aims: Long non-coding RNAs (lncRNAs) are potential biomarkers of tumors, cardiac disease, and cerebral disease because of their interaction with coding RNAs. This work focused on ischemic stroke (IS) and aimed to identify novel lncRNA biomarkers and construct lncRNA-related networks in IS. Methods: Differentially expressed lncRNAs were identified using Arraystar Human LncRNA Microarray v4.0, and validated with qRT-PCR. A lncRNA–mRNA co-expression network and a lncRNA–miRNA–mRNA regulatory network were constructed. Functional and pathway analyses were then performed. Results: In total, 560 up-regulated and 690 down-regulated differentially expressed lncRNAs were found (P < 0.05, false discovery rate < 0.05, absolute fold change ≥ 2). qRT-PCR results confirmed that lncRNA-ENST00000568297, lncRNA-ENST00000568243, and lncRNA-NR_046084 exhibited significant differential expression between IS and controls (all P < 0.05). Areas under the curves (AUCs) for these lncRNAs were 0.733, 0.743, and 0.690, respectively, and the combined AUC was 0.843. A coding–noncoding co-expression (CNC) network was constructed based on Pearson’s correlation coefficient. A specific lncRNA–miRNA–mRNA regulatory network of ENST00000568297, ENST00000568243, and NR_046084 was also constructed. Functional annotation of the up- and down-regulated mRNAs was performed. Pathway analysis enriched IS-related pathways with mRNAs in the lncRNA–miRNA–mRNA regulatory network. Conclusion: LncRNA and mRNA expression profiles in human peripheral blood were altered after IS. ENST00000568297, ENST00000568243, and NR_046084 were identified as novel potential diagnostic biomarkers of IS. Analysis of the CNC network and lncRNA–miRNA–mRNA regulatory network suggested that lncRNAs may participate in IS pathophysiology by regulating pivotal miRNAs, mRNAs, or IS-related pathways.

scholarly journals A Novel Analysis of the Differentiated Expression of Long Noncoding RNAs Profiles in Human Prostate Cancer

2020 ◽  
Author(s):  
Chuanyu Sun ◽  
Shengyang Ge ◽  
Yuanyuan Mi ◽  
Qingfeng Hu ◽  
Yijun Guo ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Cancer Biology ◽  
Expression Profiles ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Differentially Expressed ◽  
Clinical Samples ◽  
Clinical Value ◽  
Pathway Analyses ◽  
Almost All

Abstract Background: Long noncoding RNAs (lncRNAs) have crucial roles in cancer biology. Increasing numbers of evidences have indicated that lncRNAs play an important role in the pathogenesis, invasion, and metastasis in almost all kinds of cancers. But, compared with the large amounts of patients, there is rare reports that showed the differential expression of lncRNAs in prostate cancer. Methods: In this study, lncRNA expression profiles were screened in PCa, by using 5 pairs of clinical specimens in PCa and matched non-PCa tissues with lncRNA chip. To affirm further clinical value, we extended the samples consisting of another 5 tumor specimens and 7 para-cancerous/benign contrasts by qRT-PCR in top 10 up-regulated and down-regulated lncRNAs. Results: A total of 817 lncRNAs were differentially expressed between PCa tumor and para-cancerous tissues (Fold Change ≥2.0, p < 0.05): 422 were upregulated, whereas 395 were downregulated in PCa tissues. Gene ontology and KEGG pathway analyses showed that many lncRNAs were implicated in carcinogenesis. Among differentially expressed lncRNAs, lnc-MYL2-4:1 (FC = 0.00141, p = 0.01909) and NR_125857 (FC = 59.27658, p = 0.00128) had the highest magnitude of change. The subsequent qPCR confirmed the expression of NR_125857 accorded with the clinical samples.Conclusions: Our study detected a relatively novel complicated map of lncRNAs in PCa, which may have the potential to investigate for diagnosis, treatment and follow-up in PCa. Our study revealed the expression of NR_125857 in human PCa tissues was most up-regulated. Further study of these meaningful candidates are need to research deep mechanisms.

scholarly journals Differential Expression Profiles and Functional Prediction of circRNAs in Necrotizing Enterocolitis

2021 ◽  
Vol 2021 ◽  
pp. 1-9
Author(s):  
Ya Pan ◽  
Wenjuan Chen ◽  
Xiangyun Yan ◽  
Boshi Yu ◽  
Shuwen Yao ◽  
...  
Keyword(s):  
Necrotizing Enterocolitis ◽  
Binding Sites ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Functional Prediction ◽  
Mirna Sponges ◽  
Pathway Analyses ◽  
Generation Sequencing ◽  
Normal Controls

Circular RNAs (circRNAs), a novel type of noncoding RNAs, have been demonstrated to behave as microRNA (miRNA) sponges to exert their effects during pathological processes of diseases. However, the roles of circRNAs have not been explored in necrotizing enterocolitis (NEC). This study sought to identify differentially expressed circRNAs and predict their potential biological functions in NEC. circRNA expression profiles in terminal ileum from newborn rats with NEC and normal controls were explored using next-generation sequencing. In the NEC group, 53 circRNAs were significantly differentially expressed, including 9 upregulated and 44 downregulated. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were conducted, and circRNA-miRNA interaction networks were generated to predict the potential roles of circRNAs in NEC progression. Further investigation revealed that most circRNAs include miRNA binding sites and that some are implicated in NEC development. In conclusion, this study’s findings demonstrate that differentially expressed circRNAs are involved in NEC development via their interactions with miRNAs, making them prospective targets for NEC diagnosis and treatment.

scholarly journals Changes in transcriptomic and metabolomic profiles of morphotypes of Ophiocordyceps sinensis within the hemocoel of its host larvae, Thitarodes xiaojinensis

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Miaomiao Li ◽  
Qian Meng ◽  
Huan Zhang ◽  
Ruihao Shu ◽  
Yanni Zhao ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Vegetative Growth ◽  
Mapk Pathway ◽  
Morphological Changes ◽  
Growth Period ◽  
Acid Synthesis ◽  
Vegetative Development ◽  
Ophiocordyceps Sinensis ◽  
Medicinal Fungus

Abstract Background Ophiocordyceps sinensis (Berk.) is a well-known entomopathogenic and medicinal fungus. It parasitizes and mummifies the underground ghost moth larvae to produce a fruiting body named Chinese cordyceps. Specific for the fungus, O. sinensis experiences a biotrophic vegetative growth period spanning over 5 months. During this vegetative growth, it appears successively in the host hemocoel in three/four morphotypes, namely, the yeast-like blastospores (subdivided into proliferative (BP) and stationary phase (BS)), prehyphae (PreHy) and the hyphae (Hy). This peculiar morphogenesis has been elucidated through morphological and ultrastructural observations, but its molecular basis remains cryptic. In this study, transcriptome and metabolome profiling of BP, BS, PreHy and Hy stages were performed to characterize the key genes, metabolites, and signaling pathways that regulated the vegetative development of O. sinensis in Thitarodes xiaojinensis larva. Results The molecular events and metabolic pathways that regulated different intracellular processes at various stages were examined. Cluster analyses of differentially expressed genes across the four stages revealed the stage specifically enriched pathways. Analysis of metabolome profiles showed that carbon metabolism and several amino acids biosynthesis were significantly perturbed during the tested development stages of O. sinensis in the host hemocoel. Genes homologous to Saccharomyces cerevisiae MAPK cascade were significantly up-regulated during the transition from blastospore to hypha. The up-regulation of Sho1, a regulator protein, suggested nutrient starvation act a role in activation of MAPK pathway and filamentous growth. In addition, up-regulation of several fatty acid synthesis genes and their corresponding products accumulation in the samples of BS might explain more lipid droplets were observed in BS than in BP. Coupled with the up-regulation of fatty acid degradation during PreHy and Hy stages, it is presumed that lipid accumulation and mobilization play important roles in filamentous development. Conclusions This is the first report comprehensively describing developmental transcriptomics and metabolomics of O. sinensis in vivo. Our findings provide new perspectives into the key pathways and hub genes involved in morphological changes of fungus developed in the hemocoel of its host, and are expected to guide future studies on morphogenesis and morphotype changes of entomopathogenic fungi in vivo.

scholarly journals Characterization and Transcriptomic Analysis of a Novel Yellow-Green Leaf Wucai (Brassica Campestris L.) Germplasm

2020 ◽  
Author(s):  
Libing Nie ◽  
Yushan Zheng ◽  
Liting Zhang ◽  
Ying Wu ◽  
Shidong Zhu ◽  
...  
Keyword(s):  
Carbon Fixation ◽  
Brassica Campestris ◽  
Chloroplast Development ◽  
Growth Period ◽  
Transcriptome Profiling ◽  
Green Leaf ◽  
Functional Identification ◽  
Leaf Color ◽  
Leaf Type ◽  
Pathway Analyses

Abstract Background: Leaf color mutants are the ideal materials to explore the pathways of chlorophyll (Chl) metabolism, chloroplast development, and photosynthesis system. In this study, a spontaneous yellow-green leaf wucai (Brassica campestris L.) mutant “WY16-13” was identified, which exhibited yellow-green leaf color during its entire growth period. However, current understanding of the molecular mechanism underlying Chl metabolism and chloroplast development of “WY16-13” is limited.Results: Comparative transcriptome profiling was performed using leaves from the yellow-green leaf type (WY16-13) and normal green-leaf type (W16-13). A total of 54.12 million (M) (WY16-13) and 56.17 M (W16-13) reads were generated. A total of 40,578 genes were identified from the mapped libraries. We identified 3,882 differentially expressed genes (DEGs) in WY16-13 compared with wild-type W16-13 (i.e., 1,603 upregulated genes and 2,279 downregulated genes). According to the Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, these DEGs are involved in porphyrin and Chl metabolism [i.e., chlorophyllase (CLH), heme oxygenase (HO), chlorophyll(ide) b reductase (NYC), and protochlorophyllide oxidoreductase (POR) genes], carbohydrate metabolism, photosynthesis, and carbon fixation in photosynthetic organisms. Moreover, deficiency in Chl biosynthetic intermediates in the mutant revealed that the formation of the yellowing phenotype was related to the disorder of heme metabolism.Conclusions: Our results provide valuable insights into Chl deficiency in the yellow-green leaf mutant and a bioinformatics resource for further functional identification of key allelic genes responsible for differences in Chl content.

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