Table 1. Ploidy-dependent genomic difference between Emiliania huxleyi strains RCC1216/1217 and CCMP1516.
| 1N specific | 2N specific | No ploidy specificity | |
|---|---|---|---|
| Consensus absent | 471 (10.3%) | 153 (3.4%) | 154 (0.8%) |
| Present, lower CNV | 804 (17.5%) | 538 (11.8%) | 1102 (6.1%) |
| Others | 3314 (72.2%) | 3861 (84.8%) | 16 728 (93.0%) |
| Contingency analysis of absence | |
|---|---|
| X2, d.f., P-value | 1170, 2, <0.0001 |
| Rel. risk, 1N vs 2N | 3.05 (2.56–3.65, <0.0001) |
| Rel. risk, 1N vs no ploidy-spec. | 12.0 (10.0–14.3, <0.0001) |
| Rel. risk, 2N vs no ploidy-spec. | 4.39 (3.15–4.90, <0.0001) |
| Contingency analysis of present, lower CNV | |
|---|---|
| X2, d.f., P-value | 763, 2, <0.0001 |
| Rel. risk, 1N vs 2N | 1.60 (1.44–1.77, <0.0001) |
| Rel. risk, 1N vs no ploidy-spec. | 3.16 (2.90–3.44, <0.0001) |
| Rel. risk, 2N vs no ploidy-spec. | 1.98 (1.80–2.18, <0.0001) |
Abbreviations: CNV, copy number variation; Rel., relative; spec., specific.
Ploidy-specific expression is determined by 50% difference in expression level between 1N and 2N cells (P<0.05: analysis of variance (ANOVA) for microarray results and Audic–Claverie statistics for 454 read counts). Apparent absence is indicated when the best BLASTN bit scores <100 against both JGI genome assembly and CCMP1516 Illumina paired-end read contigs and competitive genome hybridization (CGH) results gave <2-fold lower signal from CCMP1516 genomic DNA (gDNA) compared with RCC1216 gDNA. The global χ2 test calculates the significance of the difference among all expression categories. Relative risk ratios are given (with 95% confidence interval and P-value for 2 × 2 χ2-tests) for 1N-specific versus 2N-specific and 1N-specific versus not ploidy-specific genes. Overall, ploidy-specific genes (considering both 1N specific and 2N specific) were more likely than not ploidy-specific genes to be absent from the CCMP1516 genome by all three measures (χ2=775, P<0.0001) and more likely than not-ploidy genes to exhibit lower copy number (χ2=628, P<0.0001). The proportions of genome content differences attributable to 1N-specific genes (60%) and 2N-specific genes (20%) were calculated from the number of 1N-specific genes (471 genes) or 2N-specific genes (153 genes) found to be absent from CCMP1516 divided by the total genes identified as absent from CCMP1516 by the consensus of JGI, Illumina and CGH measures (778 genes).