Boehmeria nivea
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA272613 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1758828_1.fastq.gz | Fastqsanger.gz | |||
| SRR1758828_2.fastq.gz | Fastqsanger.gz | |||
| SRR1758829_1.fastq.gz | Fastqsanger.gz | |||
| SRR1758829_2.fastq.gz | Fastqsanger.gz |
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Project description:Digital gene expression (DGE) analysis was performed to study differentially expressed genes (DEGs) between CK and P. coffeae challenged (CH) roots of ramie. A total of 10.16 and 8.07 million clean reads were detected in the CK and CH libraries, respectively. A total of 137 genes were identified as DEGs, 117 and 20 of them were up- and down- regulated respectively, in response to P. coffeae infection. Roots samples of Pratylenchus coffeae infected(E2) and un-infected (E1) ramie were RNA-Seq sequenced to compare differented expressed genes.
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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: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.
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Project description:Digital gene expression (DGE) analysis was performed to study differentially expressed genes (DEGs) between CK and P. coffeae challenged (CH) roots of ramie. A total of 10.16 and 8.07 million clean reads were detected in the CK and CH libraries, respectively. A total of 137 genes were identified as DEGs, 117 and 20 of them were up- and down- regulated respectively, in response to P. coffeae infection.
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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
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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.
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