Table 2.
Genes from multiple copy gene families and genes containing DTT-NIC1 TE insertions within 1kb upstream region are significantly enriched in the Nicotiana EDS network. The total number of genes used to test gene duplications and the DTT-NIC1 insertions analyses differed due to the additional filtering processes used in the former analysis. For the gene duplication analysis, we excluded all genes whose most recent duplication event was uncertain. WGT: whole genome triplication; NLD refers to Nicotiana lineage specific duplications; complete EDS refers to all of genes identified in the M4 module; conserved EDS refers to M4 genes that were significantly induced by FAC in all three species, N. attenuata, N. acuminata and N. linearis; genome-wide patterns were calculated based on all of genes that were expressed in Nicotiana leaves (normalized FPKM greater than 5 in at least three samples). Bold font color highlights the statistically significant values. Odd ratios were calculated by the following formula: Odd = (p1/[1 – p1])/(p2/[1 – p2]), where p1 is the percentage of genes that are part of the EDS network among testing group, e.g., genes from multiple gene families or genes retained from Solanaceae WGT, and p2 is the percentage of genes that are part of EDS network among all leaf expressed genes.
| # genes from multiple copy families | # genes retained from Solanaceae WGT | # genes retained NLD | Total number of genes after filtering | ||
|---|---|---|---|---|---|
| Genome wide | # genes | 9691 | 6181 | 1249 | 14,642 |
| Complete EDS | # genes | 906 | 587 | 87 | 1140 |
| Odd ratio | 1.97 | 1.45 | 0.86 | ||
| p value | < 2.2E-16 | 3.30E-10 | 0.17 | ||
| Conserved EDS | # genes | 561 | 355 | 65 | 692 |
| Odd ratio | 2.18 | 1.45 | 1.07 | ||
| p value | < 2.2E-16 | 1.71E-06 | 0.41 | ||