Transcriptional effects of rhizosphere microorganisms on shoot and roots of Arabidopsis thaliana under different light conditions

For shade-intolerant species, shade light indicates the close proximity of neighboring plants and triggers the shade avoidance syndrome (SAS), which causes exaggerated growth and reduced crop yield. We report that microbiotal root commensals(Pseudomonas fluorescens and Root918) alleviate the shade avoidance responses in Arabidopsis. To identify the functions of Pseudomonas fluorescens and Root918 during SAS, we performed RNA-seq to search for differentially expressed genes (DEGs) in different tissues by comparing the transcript levels of shoot and root parts of col0 in germ-free, Pseudomonas fluorescens and Root918 during white light and shade conditions. Wild type Arabidopsis seedlings were cultured under white light for 5 days, then inoculated with Pseudomonas fluorescens and Root918 under white light for 4 days, and finally treated under white light and shade for 4 hours to extract RNA from shoot and root samples, respectively.