## 3 Results
### Transcriptomic Analysis--Pre-Treatment and Statistics  
Initial pre-treatment for rRNA removing and quality filtering with SortMeRNA and trimmomatic, respectively, conducted to the dropping of few reads, saving between 95.34% of reads for RNA-Seq sample from liquid culture of NB-glycerol in starving phase of growth and 97.62% of the total reads for sample from liquid culture of NB-glycerol in stationary phase of growth (Table 2). Afterwards, filtered reads were mapped against the assembled genome of strain L5B5. STAR statistics showed a percentage of reads mapped between 90.74% and 94.83%, depending on the culturing condition.  
The gene expression analysis with NoiSeq led to the normalization of counts performed previously with htseq-count for the different culture conditions by means of trimmed mean  
\begin{table}
\begin{tabular}{c c c c c c} \hline
**RNA-Sample** & **Raw Reads** & **Reads after rRNA Removing** & **Filtered Reads** & **Passed Reads** & **Mapped Reads** \\ \hline SGE & 40,589,012 & 40,333,005 & 38,932,275 & 95.92\% & 94.46\% \\ SGS & 31,304,717 & 31,221,230 & 30,076,663 & 96.08\% & 94.17\% \\ GYS & 31,931,209 & 31,583,884 & 30,443,705 & 95.34\% & 90.74\% \\ GLY & 35,637,786 & 35,492,545 & 34,789,606 & 97.62\% & 94.06\% \\ GLU & 33,422,936 & 32,805,879 & 32,587,198 & 97.50\% & 93.38\% \\ MAN & 32,739,745 & 32,624,884 & 31,908,361 & 97.46\% & 94.83\% \\ FRU & 33,195,686 & 33,098,880 & 32,344,406 & 97.44\% & 93.90\% \\ \hline \end{tabular}  
* SGE: Solid culture of NA-Glycerol in exponential phase of growth; SGS: Solid culture of NA-Glycerol in stationary phase of growth; GYS: Liquid culture of NB-Glycerol in death phase of growth; GLY: Liquid culture of NB-Glycerol in stationary phase of growth; GLU: Liquid culture of NB-Glucose in stationary phase of growth; MAN: Liquid culture of NB-Manrose in stationary phase of growth; FRU: Liquid culture of NB-Fructose in stationary phase of growth.  
\end{table}
Table 2: RNA-Seq statistics.  
of M-values (TMM) with the filtration of 90% of less expressed genes (622 genes highly expressed genes), to get a minimum of 6080 counts per genome feature or predicted gene. Focusing on condition datasets, liquid cultures in stationary phase of growth had more genes being over this cut-off than observed in other conditions. Thus, the sample from liquid culture with fructose in stationary phase (FRU) was the dataset with more genes overexpressed, whereas the sample from solid culture with glycerol in stationary phase (SGS) was the smaller dataset. The largest set of overexpressed genes was shared among the seven sample's genes independently of the culture conditions and bacterial phases of growth, including 199 genes (Figure 7). Afterwards, liquid culture conditions, including both stationary and death phases, derived in 69 shared features, were followed for samples from liquid culture and stationary phase, when any source carbon was used, equally, with 42 shared genes. To summarize, the variations in culture conditions had a greater incidence in the differential expression of genes analysis, as observed with the solid and liquid cultures, with respect to what was observed when the bacterium phases of growth were evaluated for _Pseudomonas_ sp., strain L5B5. On the contrary, the assays using alternative carbon sources showed a low incidence in the differential expression of genes.  
Figure 7: Relation of overexpressed genes between conditions for _Pseudomonas_ sp., strain L5B5. The figure represents those genes within the 90% of overexpressed genes. SGS: Solid culture. NA-Glycerol. Stationary phase of bacterial growth; SGE: Solid culture. NA-Glycerol. Exponential phase of bacterial growth; GYS: Liquid culture. Nutrient broth with glycerol. Dead phase of growth; GLY: Liquid culture. NB-Glycerol. Stationary phase of growth; GLU: Liquid culture. NB-Glucose. Stationary phase of growth; MAN: Liquid culture. NB-Mannose. Stationary phase of growth; FRU: Liquid culture. NB-Fructose. Stationary phase of growth.