Table 1.
Statistical test results on TE insertions in DE versus non-DE genes, and in DE genes previously described as underlying CAM, glycolysis, or starch metabolism, versus all other genes
| Total number of genes with 1 or more TE insertions | ||||||
|---|---|---|---|---|---|---|
| T. fasciculata | T. leiboldiana | |||||
| All genes | DE genes | CAM-DE genes | All genes | DE genes | CAM-DE genes | |
| All TEs (intronic only) | 15,844 (50%) | 473 (52%) | 28 (41.2%) | 10,348 (51%) | 387 (54%) | 21 (36.2%)a |
| All TEs | 22,969 (90%) | 725 (91%) | 58 (85%) | 18,512 (91%) | 665 (92%) | 50 (86%) |
| DNA transposons | 16,857 (66%) | 556 (70%) | 45 (66%) | 14,463 (71%) | 547 (76%)b | 42 (72%) |
| Helitrons | 17,388 (69%) | 561 (70%) | 47 (69%) | 14,701 (72%) | 530 (74%) | 38 (65%) |
| LTR-Copia | 11,147 (44%) | 353 (44%) | 28 (41%) | 10,487 (51%) | 394 (55%) | 31 (53%) |
| LTR-Gypsy | 10,365 (41%) | 341 (43%) | 22 (32%) | 5,399 (26%) | 199 (28%) | 10 (17%) |
| Average and (median) TE insertion counts per gene | ||||||
| T. fasciculata | T. leiboldiana | |||||
| Non-DE genes | DE genes | CAM genes | Non-DE genes | DE genes | CAM genes | |
| All TEs (intronic only) | 2.90 (1) | 3.71 (1)a | 2.618 (0) | 3.24 (1) | 3.96 (1)b | 2.862 (0) |
| All TEs | 6.79 (5) | 7.83 (6)b | 6.32 (5) | 7.62 (5) | 8.75 (6)c | 7.36 (5) |
| DNA transposons | 2.15 (1) | 2.56 (2)c | 2.03 (1) | 2.49 (2) | 2.97 (2)c | 2.77 (2) |
| Helitrons | 1.97 (1) | 2.27 (2)c | 2.12 (1) | 2.43 (2) | 2.72 (2)a | 2.12 (1) |
| LTR-Copia | 1.00 (0) | 0.95 (0) | 0.87 (0) | 1.22 (1) | 1.45 (1)b | 1.25 (1) |
| LTR-Gypsy | 0.92 (0) | 1.09 (0) | 0.76 (0) | 0.61 (0) | 0.65 (0) | 0.39 (0) |
TE insertions were counted in intronic + 3-kb upstream regions, but insertions in introns only are also shown. aP > 0.05, bP > 0.01, cP > 10–3.