Genomic, transcriptomic, and proteomic approaches towards understanding the molecular mechanisms of salt tolerance in Frankia strains isolated from Casuarina trees

Table 2 qRT-PCR validation of RNA-seq data

Locus tag	qRT-PCR fold change (salt stress vs control)	RNAseq fold change (salt stress vs control)	RNAseq vs qRT-PCR p-value (salt stress)	qRT-PCR fold change (osmotic stress)	RNAseq fold change (osmotic stress)	RNAseq vs qRT-PCR p-value (osmotic stress)
CCI6_RS21730^a	2.100^e	2.360	0.840	1.100	−6.000	0.012^d
CCI6_RS17915^a	3.120^e	3.240	0.960	1.820^e	1.980	0.870
CCI6_RS19875^a	2.500^e	4.910	0.03^d	3.011^e	11.210	0.023^d
CCI6_RS17580^a	3.140^e	3.480	0.870	2.120^e	1.520	0.560
CCI6_RS16000^a	1.890^e	2.183	0.930	−0.500	−1.200	0.040^d
CCI6_RS18570^c	1.320	1.230	0.240	1.511	1.380	0.720
CCI6_RS06495^c	1.400	1.500	0.450	−1.310	−2.020	0.220
CCI6_RS02325^b	3.500^e	3.840	0.830	2.800^e	3.860	0.620
CCI6_RS12340^c	−1.300	−4.000	0.023^d	1.300	−9.000	0.026^d
CCI6_RS08505^a	3.230^e	3.590	0. 753	1.150	1.051	0.972
CCI6_RS19950^b	10.021	12.061	0.778	18.231	21.585	0.812

^aUp-regulated genes under salt stress according to RNA-Seq analysis
^bUp-regulated genes under both conditions according to RNA-Seq analysis
^cNon-differentially expressed genes in the study according to RNA-Seq analysis
^dIndicates that there is a statistically significant difference between fold change values determined by qPCR and RNA-seq
^eIndicates a statistically significant qRT-PCR fold change value
The fold change values (salt vs control or sucrose vs control) determined from the RNAseq experiment were compared with the fold change values obtained from qRT-PCR experiments. For the qRT-PCR experiments, the ∆∆C_t method was used to determine the fold change. The rpsA gene was used as the normalizer for all of the qRT-PCR experiments. The fold change values for the RNA-seq experiments are based on two biological replicates whereas the fold change values for the qRT-PCR experiments are based on three biological replicates

ISSN: 1471-2164