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Genome-wide expression analysis of ramie [Boehmeria nivea (L.) Gaudich] genes in response to ramie moth [Cocytodes coerulea Guenée] infestation

ABSTRACT: Comparative transcriptome analysis was performed to study differentially expressed genes (DEGs) between Cocytodes caerulea Guenée challenged (CH) and unchallenged (CK) leaves of ramie.We obtained 40.2 and 62.8 million reads for CH and CK libraries respectively.De novo assembling of these reads generated 26,759 and 29,988 unigenes respectively. After a integrate assembly for all data of these two libraries, a total of 46,533 unigenes with an average length of 845 bp were obtained.A total of 1179 genes were identified as DEGs, 657 and 1230 of them were up- and down- regulated respectively, in response to C.caerulea infestation.

ORGANISM(S): Boehmeria nivea

PROVIDER: GSE66447 | GEO | 2015/03/04

SECONDARY ACCESSION(S): PRJNA276975

REPOSITORIES: GEO

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Identification of drought stress-responsive transcription factor in ramie (Boehmeria nivea L．Gaud)

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.

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Genome-wide transcriptional changes of ramie (Boehmeria nivea LM-oM-<M-^NGaud) in response to the infection of root-lesion nematode

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Transcriptome Analysis of Ramie (Boehmeria nivea L. Gaud.) in Response to Ramie Moth (Cocytodes coerulea Guenee) Infestation.

Project description:The ramie moth Cocytodes coerulea Guenée (RM) is an economically important pest that seriously impairs the yield of ramie, an important natural fiber crop. The molecular mechanisms that underlie the ramie-pest interactions are unclear up to date. Therefore, a transcriptome profiling analysis would aid in understanding the ramie defense mechanisms against RM. In this study, we first constructed two cDNA libraries derived from RM-challenged (CH) and unchallenged (CK) ramie leaves. The subsequent sequencing of the CH and CK libraries yielded 40.2 and 62.8 million reads, respectively. Furthermore, de novo assembling of these reads generated 26,759 and 29,988 unigenes, respectively. An integrated assembly of data from these two libraries resulted in 46,533 unigenes, with an average length of 845 bp per unigene. Among these genes, 24,327 (52.28%) were functionally annotated by predicted protein function. A comparative analysis of the CK and CH transcriptome profiles revealed 1,980 differentially expressed genes (DEGs), of which 750 were upregulated and 1,230 were downregulated. A quantitative real-time PCR (qRT-PCR) analysis of 13 random selected genes confirmed the gene expression patterns that were determined by Illumina sequencing. Among the DEGs, the expression patterns of transcription factors, protease inhibitors, and antioxidant enzymes were studied. Overall, these results provide useful insights into the defense mechanism of ramie against RM.

| S-EPMC4789370 | biostudies-literature

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