E-GEOD-51900 - Genome-wide transcriptional changes of ramie (Boehmeria nivea L.Gaud) in response to the infection of root-lesion nematode

Released on 28 April 2014, last updated on 29 May 2014
Boehmeria nivea
Samples (4)
Protocols (3)
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.
Experiment type
RNA-seq of coding RNA 
Touming Liu
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-GEOD-51900.idf.txt
Sample and data relationshipE-GEOD-51900.sdrf.txt