Expression profiling of ramie genes
Ontology highlight
ABSTRACT:
ORGANISM(S): Boehmeria nivea
PROVIDER: GSE158630 | GEO | 2020/09/29
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptome analysis of root development related genes in terrestrial and hydroponic ramie. Ramie seedlings were cultivated in soil, and in hydroponic with the shoot-cutting propagation method. The root samples from hydrophonic ramie were collected from the early stage (5-day-old seedling) and the late stage (30-day-old seedling) of acquatic roots induction. The roots of ramie seedling cultivated in soil were also collected for comparative analysis. Our study represents the detailed analysis of ramie root transcriptomes with biologic replicates.
2017-09-15 | GSE98903 | GEO
Project description:The Root-lesion nematode (RLN) Pratylenchus coffeae is a major ramie pest causing severe fiber yield loss annual in China. The response mechanism of ramie to RLN-infection is poorly understood. Two RLN-infected plants (Inf1 and Inf2) and two control plants (CO1 and CO2) were individually used to sequence by Illumina pair-end sequencing. About 56.3, 51.7, 43.4 and 45.0 million sequencing reads were generated from the libraries of CO1, CO2, Inf1 and Inf2, respectively. De novo assembly for these 196 million reads yielded 50,486 unigenes with an average length of 853.3 bp. Based on sequence similarity search with known proteins, a total of 24,820 (49.2%) genes were annotated for their function. Comparison of gene expression level between CO and Inf ramie based on the normalized value of read counts per kilobase of exon model per million reads (RPKM) revealed that there were 777 differentially expressed genes (DEGs). Further, these functional category of DEGs were classified by assigning them to gene ontology (GO) and clusters of orthologous group (COG). Pathway enrichment analysis showed that three pathways (Phenylalanine metabolism, Carotenoid biosynthesis and Phenylpropanoid biosynthesis) were severely influenced by RLN-infection. The genome-wide expression profiling of ramie responding to RLN-infection was first characterized. A series of candidate genes and pathways that may contribute to defense response against RLN in ramie will be helpful for further improving the resistance to RLN-infection.
2014-04-28 | GSE51900 | GEO
Project description:Drought is a main environment stress which severely inhibits the stem growth of ramie and lead to a decrease of the fiber yield. The mechanisms of ramie responding to drought stress are poorly understood. Using Illumina sequencing, approximately 4.8 million (M) 21-nt cDNA tags were sequenced in the cDNA library derived from the drought-stressed ramie (DS), and about 4.7 M were sequenced in the cDNA library constructed from the control ramie under well water condition (CO). The tags generated from two libraries were aligned with ramie transcriptome to annotate their function and a total of 23,912 and 22,826 ramie genes were matched by these tags of DS and CO library, respectively. Comparison of gene expression level between CO and DS ramie based on the differences of tag frequencies appearing in two libraries revealed that 1101 and 505 genes were respectively up- and down- regulated under drought stress. Pathway enrichment analysis identified a set of significantly enriched pathways of DEGs. A series of candidate genes and pathways that may contribute to drought tolerance in ramie will be helpful for further improving ramie drought tolerance ability.
2013-04-23 | GSE46253 | GEO
Project description:The Root-lesion nematode (RLN) Pratylenchus coffeae is a major ramie pest causing severe fiber yield loss annual in China. The response mechanism of ramie to RLN-infection is poorly understood. Two RLN-infected plants (Inf1 and Inf2) and two control plants (CO1 and CO2) were individually used to sequence by Illumina pair-end sequencing. About 56.3, 51.7, 43.4 and 45.0 million sequencing reads were generated from the libraries of CO1, CO2, Inf1 and Inf2, respectively. De novo assembly for these 196 million reads yielded 50,486 unigenes with an average length of 853.3 bp. Based on sequence similarity search with known proteins, a total of 24,820 (49.2%) genes were annotated for their function. Comparison of gene expression level between CO and Inf ramie based on the normalized value of read counts per kilobase of exon model per million reads (RPKM) revealed that there were 777 differentially expressed genes (DEGs). Further, these functional category of DEGs were classified by assigning them to gene ontology (GO) and clusters of orthologous group (COG). Pathway enrichment analysis showed that three pathways (Phenylalanine metabolism, Carotenoid biosynthesis and Phenylpropanoid biosynthesis) were severely influenced by RLN-infection. The genome-wide expression profiling of ramie responding to RLN-infection was first characterized. A series of candidate genes and pathways that may contribute to defense response against RLN in ramie will be helpful for further improving the resistance to RLN-infection. A total of four samples, two replicates of control plant (CO1 and CO2) and two replicates of RLN-infected plants (Inf1 and Inf2) were used for RNA-seq.
2014-04-28 | E-GEOD-51900 | biostudies-arrayexpress
Project description:Drought is a main environment stress which severely inhibits the stem growth of ramie and lead to a decrease of the fiber yield. The mechanisms of ramie responding to drought stress are poorly understood. Using Illumina sequencing, approximately 4.8 million (M) 21-nt cDNA tags were sequenced in the cDNA library derived from the drought-stressed ramie (DS), and about 4.7 M were sequenced in the cDNA library constructed from the control ramie under well water condition (CO). The tags generated from two libraries were aligned with ramie transcriptome to annotate their function and a total of 23,912 and 22,826 ramie genes were matched by these tags of DS and CO library, respectively. Comparison of gene expression level between CO and DS ramie based on the differences of tag frequencies appearing in two libraries revealed that 1101 and 505 genes were respectively up- and down- regulated under drought stress. Pathway enrichment analysis identified a set of significantly enriched pathways of DEGs. A series of candidate genes and pathways that may contribute to drought tolerance in ramie will be helpful for further improving ramie drought tolerance ability. 3' tag-based DGE libraries were generated to exam the differentially expressed gene between drought-stressed and well-watered ramie
2013-04-23 | E-GEOD-46253 | biostudies-arrayexpress
Project description:Two ramie cultivars, Zhongzhu no 2(Z2) and Huazhu no 4 (H4), showed constructing adventitious root formation (ARF) rate. Comparative transcriptome analysis was performed to study gene expression profiles in Z2 and H4 ramie during adventitious root formation. Illumina sequencing yielded a total of 92,794,556,688 bases data, and about 301.47 M and 313.06 M raw reads for Z2 and H4 plants, respectively. After quality control, every library obtained over 43 million reads, which is enough for the quantitative analysis of gene expression. Using Trinity software, these clean reads were first assembled into 121,492 transcripts, finally into 66,881 unigenes with an average length of 1144.25 bp. About 148.74 M and 138.72 M clean reads of H4 and Z2 were mapped to reference genes via Bowtie, respectively. The ratio of mapped clean reads for eight libraries ranged from 74.47% to 75.38% (average: 74.8%). By comparing gene expression levels in Tm and CK ramie stems, we identified 772 DEGs in H4 plants during RPF, including 7220 up-regulated and 8154 down-regulated DEGs. We identified 1256 DEGs in Z2 plants during RPF, which included 779 up-regulated and 447 down-regulated DEGs. We also identified 1919 DEGs between Z2 and H4 plants. There were 1147 (731 up-regulate and 416 down-regulated) DEGs uniquely in Z2, and 603 (202 up-regulate and 461 down-regulated) DEGs uniquely in H4 plants. The two genotypes shared 109 DEGs, which indicates some common pathways during ARF.
2019-06-20 | GSE116063 | GEO
Project description:Ramie fibers extracted from the stem barks have been utilized for thousands years in China, and its biosynthetic mechanism is poorly understood. Here, we have characterized and compared the expression profiling of the barks from the top and middle part of stem where the secondary cellular walls (SCWs) of fiber cell have not initiated growth and was thickening, respectively; resulting in 4,520 differential expression (DE) protein-coding transcripts (PCTs), 1,287 DE long noncoding RNAs (lncRNAs), 88 DE miRNAs and 78 DE circular RNAs (circRNAs). Among the 4,520 DE PCTs, 75 were identified to be the homolog of the Arabidopsis SCW-biosynthetic genes. Overexpression of whole_GLEAN_10014861 (a homolog of SND1) in Arabidopsis caused a significant up-regulation in the expression of AtMYB46 and AtMYB83 that are two key regulators for SCW biosynthesis, thus conferring more fiber cells, along with a remarkable thickening in the SCWs of these cells. Bioinformatic prediction revealed 14 of the 75 homolog targeted by 16 noncoding RNAs (including 8 miRNAs and 8 lncRNAs), and two involved in the competing endogenous RNAs networks, indicating a complex regulatory network for the SCW biosynthesis of bast fiber in ramie. This study provides important insights into the bast fiber biosynthesis of ramie.
2019-05-02 | GSE130587 | GEO
Project description:Cadmium (Cd)-contamination in soil has been becoming a major environmental problem in China. Ramie, a fiber crop, was frequently proposed to be used as the crop for phytoremediation of Cd-contaminated farmlands. However, high level Cd accumulation can cause a great inhibition of growth in ramie. To understand the potential mechanism for this phenomenon, the ramie genes involved in the Cd stress response were identified using Illumina pair-end sequencing in two Cd-stressed plants (CdS1 and CdS2) and two control plants (CO1 and CO2) in this study. Approximately 48.7, 51.6, 41.2, and 47.1 million clean sequencing reads generated from the libraries of CO1, CO2, CdS1, and CdS2, respectively, were De novo assembled to yield 56,932 non-redundant unigenes. A total of 26,686 (46.9%) genes were annotated for their function. Comparison of gene expression levels between CO and CdS ramie revealed 155 differentially expressed genes (DEGs). Sixteen DEGs was further confirmed their expression difference by real-time quantitative PCR (qRT-PCR). Among these 16 DEGs, 2 genes encoding GA2-oxidase which is a major enzyme for deactivating bioactive gibberellins (GAs) were found with a markedly up-regulated expression, which is possibly responsible for the growth inhibition of Cd-stressed ramie. Pathway enrichment analysis revealed that a pathway (Cutin, suberine and wax biosynthesis) was markedly enriched by DEGs. The discovery of these Cd stress-responsive genes and pathways will be helpful for further understanding the mechanism of Cd-stressed response and improving the ability of Cd stress tolerance in ramie.
2015-08-21 | GSE60583 | GEO
Project description:Ramie is an important natural fiber crop. Drought is an abiotic stress that strongly influences plant growth, development and productivity. There has been little research on the molecular mechanisms of ramie related to drought and then it is poorly understood. In this study, we conducted for the first time an iTRAQ-based (isobaric tags for relative and absolute quantitation) comparative proteomic analysis
2016-10-05 | PXD001940 | Pride
Project description:This project intends to conduct comparative proteomics research on wild and cultivated varieties of Dendrobium huoshanense that are similar in plant shape and in the same growth and development stage through proteomics and protein modification omics combined with the differences in metabolites in Dendrobium huoshanense. Full-scan proteomic data of Dendrobium; compare the protein expression levels of wild and cultivated varieties to find relevant candidate proteins, and perform functional annotation and KEGG analysis of metabolic pathways for candidate proteins with different expressions to further analyze the material basis differences between wild and cultivated varieties Provide research objects of molecular biology.
2022-06-24 | PXD022337 | Pride