Table 1.
Primers used for validation of RNA-seq transcriptome by RT-qPCR.
Table 2.
Data from the RNA-seq analysis for P. tropica strain PPe8 grown in presence and absence of apoplast fluid from sugarcane variety RB867515.
Fig 1.
Correlation analysis between RNA-seq and RT-qPCR analysis of the differential genes expression in Ppe8 strain in MLA medium in comparasion with MM medium (calibrator = 1).
The data of RT-qPCR were expressed in relative expression and the data of RNA-seq in fold change.
Table 3.
Genes differentially expressed in the P. tropica strain Ppe8, grown in MM (defined medium) (calibrator = 1) in comparison to MLA (apoplast fluid medium).
Fig 2.
Functional classification of genes upregulated and downregulated in strain Ppe8 grown in presence of sugarcane apoplast fluid.
One hundred fifty-three were upregulated (A) and 544 were downregulated (B) in presence of apoplast fluid. The genes were functionally classified by COG (Clusters of Orthologous Groups of Proteins) (http://www.ncbi.nlm.nih.gov/COG), [28].
Fig 3.
Genes of the cell motility and chemotaxis are repressed in strain Ppe8 grown in the presence of apoplast fluid in comparasion with defined medium.
Genes without bars (Fold change) were not differentially expressed. The genes with fold change equal or minor that -2 were considered repressed in strain Ppe8 in presence of sugarcane apoplast fluid.
Fig 4.
Regulatory cascade of chemotaxis (Source: Adapted from Russell, 2012 [29]).
The genes depicted in the figures that participate of chemotaxis in Ppe8 strain, were repressed in the presence of apoplast fluid in comparasion with defined medium. The genes with fold change equal or minor that -2 were considered repressed in strain Ppe8 in presence of sugarcane apoplast fluid.
Fig 5.
Proteins involved in flagellar assembly (Source: Adapted from KEGG[30]).
The set of genes present in genome of P. phytofirmans is represented in the green box. This genome is one of the closest, phylogenetically, to plant endophytic Paraburkholderia species that have been published. Genes that are in the light red boxes were repressed in strain Ppe8 in the presence of apoplast fluid in comparation with defined medium. The genes with fold change equal or minor that -2 were considered repressed in strain Ppe8 in presence of sugarcane apoplast fluid. Reprinted from Kanehisa et al. under a CC BY license, with permission from KEGG, original copyright [2016].