Table 3. Validation of RNA-Seq results using quantitative PCR analysis.

Locus ID CCEa	Orthologues J2315b	Descriptionc	gene name	wt vs rpfF d	wt vs rpfF comple	wt vs cepR f	wt vs cepR complg
CCE46720	BCAM0186	Fucose-Binding lectin protein	bclA	74	1.2	4.1	0.4
CCE48446	BCAM0581	Enoyl-CoA hydratase/carnithine racemase	rpfF	0.6	0.3	0.7	0.8
CCE48447	BCAM0580	EAL/GGDEF domain protein	rpfR	1	0.6	0.8	0.5
CCE50322	BCAM1870	N-acyl-L-homoserine lactone synthetase	cepI	3.2	1.6	65.0	0.8
CCE50324	BCAM1868	Transcriptional regulator protein	cepR	1.7	1.8	0.6	0.3
CCE50476	BCAL2353	Sulfate permease		6	1.8	4.2	1.1
CCE50898	BCAM0854	Mannose-6-phosphate isomerase		11.3	1	6.3	0.6
CCE52109	BCAS0293	AidA	aidA	6	1.8	685.0	0.5

^aNomenclature according to GenBank file CAFQ01000001.1.

^bOrthologs were identified as described in the Material and Methods section.

^cDescription according to EggNOG classification.

^dFold change (FC) of expression, comparing wild type strain with rpfF mutant grown in LB medium until an OD of 2.

^eFold change (FC) of expression, comparing wild type strain with complemented rpfF mutant grown in LB medium until an OD of 2.

^fFold change (FC) of expression comparing wild type strain with cepR mutant grown in LB medium until an OD of 2.

^gFold change (FC) of expression, comparing wild type strain with complemented cepR mutant grown in LB medium until an OD of 2.