Table S2: Ranking of reference genes suitable for ...

Table  S2:  Ranking  of  reference  genes  suitable  for  normalization  of  stress  adaptation  models  by  comparison  of  expression  levels  between  one  stress  condition  (either  NaCl  or  acidic  stress)  and  the  control  condition  without  stress. Adaptation  model LB  compared  to  LB+NaCl

Software BestKeeper SD r p geNorm M

CYGP  compared  to  CYGP+NaCl BestKeeper SD r p geNorm M LB  compared  to  LB+acid

BestKeeper SD r p geNorm M

CYGP  compared  to  CYGP+acid BestKeeper (without  KLT_6)2

SD r p

geNorm M

Ranking 1 rplD 0.87 0.978 0.001 rplD 0.548 rho 0.91 0.954 0.001 rho 0.714 rplD 0.88 0.976 0.001 rplD 0.613

2 rpoB 0.88 0.968 0.001 rho 0.578 gyrB 0.82 0.930 0.001 rpoB 0.739 rpoB 0.79 0.945 0.001 rho 0.684

3 rho 0.83 0.956 0.001 rpoB 0.580 rpoB 0.79 0.918 0.001 gyrB 0.746 gyrB 0.99 0.926 0.001 rpoB 0.691

4 gyrB 0.88 0.897 0.001 pyk 0.675 proC 0.81 0.896 0.001 proC 0.761 rho 0.84 0.990 0.001 gyrB 0.743

rho

proC

ftsZ

gyrB

0.97 0.928 0.001

1.00 0.901 0.001

0.86 0.816 0.001

0.99 0.593 0.001

rho

rpoB

proC

ftsZ

(rplD)3

0.892

0.910

1.011

1.021

1.069

5 ftsZ 0.97 0.862 0.001 gyrB 0.688 ftsZ 0.90 0.874 0.001 ftsZ 0.831 proC 0.63 0.743 0.001 pyk 0.771

6 proC 0.83 0.843 0.001 proC 0.719 16S  rRNA 0.47 0.521 0.001 rplD 0.838 ftsZ 0.98 0.711 0.001 proC 0.883

7 16S  rRNA 0.54 0.596 0.001 ftsZ 0.792

recA 0.941 16S  rRNA 0.54 0.668 0.001 ftsZ 0.892

8

9

recA 0.984

16S  rRNA 0.992

RG1

2

3

16S  rRNA 0.956

recA 0.975

2

5

1)  n  RG  =  number  of  reference  genes  recommended  by  geNorm 2)  When  all  nine  reference  gene  candidates  were  included,  Bestkeeper  determined  that  only  ftsZ  would  be  suitable  as  a  reference  gene  (SD  =  0.96,  r  =  0.880,  p  =  0.001).  Results  listed  depict  the  BestKeeper  ranking  of  reference  genes,  when  strain  KLT_6  leading  to  the  most  variable  results  was  excluded. 3)  geNorm  suggested  the  use  of  five  reference  genes  for  normalization  of  stress  adaptation  experiments  in  CYGP  w/o  glucose.  However,  only  four  genes  met  all  standards  required  by  the  software,  with  rplD  representing  the  best  performing  gene  among  the  excluded  HKGs.