Next Generation Sequencing of grapevine wood pathogen infection in the presence of a root biocontrol agent.

ABSTRACT: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) from grapevine wood infected by a fungal pathogen in the presence of a root biological control agent. One of the goals was to obtain molecular data about the fungus pathogen (Phaeomoniella chlamydospora) during grapevine wood infection. Grapevine pathogen-infected wood mRNA profiles of 2-month-old plantlets (14 days post infection) were generated by deep sequencing, in triplicate, using Illumina Hiseq2500. The sequence reads that passed quality filters were analyzed by TopHat followed by Cufflinks. qRTaPCR validation was performed using SYBR Green assays. Using an optimized data analysis workflow, we mapped sequence reads to the grapevine genome (build IGGP 12x) and identified pathogen transcripts. RNAse

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Vitis vinifera

SUBMITTER: Noel MAGNIN 

PROVIDER: E-MTAB-3966 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress