Dataset Information

Transcriptome analysis of woodland strawberry (Fragaria vesca) response to the infection by Strawberry vein banding virus (SVBV).

ABSTRACT:

Background

Woodland strawberry (Fragaria vesca) infected with Strawberry vein banding virus (SVBV) exhibits chlorotic symptoms along the leaf veins. However, little is known about the molecular mechanism of strawberry disease caused by SVBV.

Methods

We performed the next-generation sequencing (RNA-Seq) study to identify gene expression changes induced by SVBV in woodland strawberry using mock-inoculated plants as a control.

Results

Using RNA-Seq, we have identified 36,850 unigenes, of which 517 were differentially expressed in the virus-infected plants (DEGs). The unigenes were annotated and classified with Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The KEGG pathway analysis of these genes suggested that strawberry disease caused by SVBV may affect multiple processes including pigment metabolism, photosynthesis and plant-pathogen interactions.

Conclusions

Our research provides comprehensive transcriptome information regarding SVBV infection in strawberry.

SUBMITTER: Chen J

PROVIDER: S-EPMC4942977 | biostudies-literature | 2016 Jul

REPOSITORIES: biostudies-literature

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Publications

Transcriptome analysis of woodland strawberry (Fragaria vesca) response to the infection by Strawberry vein banding virus (SVBV).

Chen Jing J Zhang Hanping H Feng Mingfeng M Zuo Dengpan D Hu Yahui Y Jiang Tong T

Virology journal 20160713

<h4>Background</h4>Woodland strawberry (Fragaria vesca) infected with Strawberry vein banding virus (SVBV) exhibits chlorotic symptoms along the leaf veins. However, little is known about the molecular mechanism of strawberry disease caused by SVBV.<h4>Methods</h4>We performed the next-generation sequencing (RNA-Seq) study to identify gene expression changes induced by SVBV in woodland strawberry using mock-inoculated plants as a control.<h4>Results</h4>Using RNA-Seq, we have identified 36,850 u ...[more]

PMID: 27411713

Similar Datasets

Project description:BackgroundFragaria vesca is a low-growing, small-fruited diploid strawberry species commonly called woodland strawberry. It is native to temperate regions of Eurasia and North America and while it produces edible fruits, it is most highly useful as an experimental perennial plant system that can serve as a model for the agriculturally important Rosaceae family. A draft of the F. vesca genome sequence was published in 2011 [Nat Genet 43:223,2011]. The first generation annotation (version 1.1) were developed using GeneMark-ES+[Nuc Acids Res 33:6494,2005]which is a self-training gene prediction tool that relies primarily on the combination of ab initio predictions with mapping high confidence ESTs in addition to mapping gene deserts from transposable elements. Based on over 25 different tissue transcriptomes, we have revised the F. vesca genome annotation, thereby providing several improvements over version 1.1.ResultsThe new annotation, which was achieved using Maker, describes many more predicted protein coding genes compared to the GeneMark generated annotation that is currently hosted at the Genome Database for Rosaceae ( http://www.rosaceae.org/ ). Our new annotation also results in an increase in the overall total coding length, and the number of coding regions found. The total number of gene predictions that do not overlap with the previous annotations is 2286, most of which were found to be homologous to other plant genes. We have experimentally verified one of the new gene model predictions to validate our results.ConclusionsUsing the RNA-Seq transcriptome sequences from 25 diverse tissue types, the re-annotation pipeline improved existing annotations by increasing the annotation accuracy based on extensive transcriptome data. It uncovered new genes, added exons to current genes, and extended or merged exons. This complete genome re-annotation will significantly benefit functional genomic studies of the strawberry and other members of the Rosaceae.

Dataset Information

Transcriptome analysis of woodland strawberry (Fragaria vesca) response to the infection by Strawberry vein banding virus (SVBV).

Background

Methods

Results

Conclusions

Publications

Transcriptome analysis of woodland strawberry (Fragaria vesca) response to the infection by Strawberry vein banding virus (SVBV).

Similar Datasets

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