Table 4.
Transcripts at lower levels in stationary (high-toxin-producing) as compared to late-exponential (low-toxin-producing) phase in Pseudo-nitzschia multiseries ( Ps-n ) as determined by cDNA microarray analysis
| |
|
Fold change
a
|
|
||
|---|---|---|---|---|---|
|
Stationary versus late-exponential phase | |||||
|
Ps-n
NR Identifier |
JGI
Ps-n
Genome Hit |
Non-axenic |
Non-axenic |
Axenic |
Predicted gene product |
| Scaffold:Start-End | Expt. 1 | Expt. 2 | Expt. | ||
| PSN0100 |
32:397085-398987 |
0.34 ± 0.01 |
0.33 ± 0.05 |
0.39 ± 0.01 |
Pyrophosphate-dependent phosphofructokinase (PFK) |
| PSN0060 |
133:16659-18505 |
0.20± 0.02 |
0.16 ± 0.03 |
0.44 ± 0.04 |
Predicted protein with signal or transit peptide |
| PSN0048 |
188:179178-180986 |
0.36± 0.08 |
0.25 ± 0.06 |
0.52 ± 0.05 |
Predicted protein with signal or transit peptide |
| PSN0080 |
461:123066-124152 |
0.32 ± 0.02 |
0.33 ± 0.03 |
0.57 ± 0.07 |
Predicted protein with mitochondrial transit peptide |
| 135E4 |
1441:17433-18891 |
0.17 ± 0.00 |
0.19 ± 0.02 |
0.45 ± 0.02 |
Predicted protein |
| 165G9 |
8:175639-176910 |
0.37 ± 0.02 |
0.37 ± 0.02 |
0.62 ± 0.04 |
Tetratricopeptide repeat protein |
| 135H6b |
214:78592-7971 |
0.41 ± 0.00 |
0.22 ± 0.02 |
0.59 ± 0.00 |
Fucoxanthin-chlorophyll a-c binding protein, |
| chloroplastic (FCP) | |||||
aThe fold-change data presented are the average of all of the cDNA clones that were printed on the array for each transcript. The number of cDNA clones for each transcript was: PSN0100 (2), PSN0060 (5), PSN0048 (5), PSN0080 (3), 135E4 (1), 165G9 (1), 135H6 (1), and each clone was printed twice.
b135H6 was included as a gene of interest in RT-qPCR analysis, below, although it did not meet our fold-change cut-off for the original FDR microarray analysis (yet, all LFDRs were <10%). Please see Methods for statistical analysis, and Additional file 1 for FDR and LDFR data.