Table I. Characteristics of the transcriptomes sequenced.
| Sample | Total Reads | Mean Quality Score | Mapped Reads | Genes Expresseda | Up-Regulatedb | Down-Regulatedb |
|---|---|---|---|---|---|---|
| A. thaliana mature pistils unpollinated | 109,362,994 | 36.51 | 89,537,597 | 69.79 | ||
| A. thaliana pistils selfed 8 HAP | 101,942,362 | 36.52 | 96,071,451 | 69.06 | 81 (0.28) | 260 (0.90) |
| A. thaliana pistils × A. lyrata pollen 8 HAP | 100,332,498 | 36.84 | 95,899,345 | 68.89 | 181 (0.63) | 296 (1.03) |
| A. thaliana pistils × A. halleri pollen 8 HAP | 103,676,026 | 36.9 | 98,639,610 | 69.28 | 211 (0.73) | 297 (1.03) |
| A. thaliana pistils 3 DAI with Fusarium | 97,213,704 | 36.59 | 70,661,826 | 65.38 | 1,928 (6.73) | 2,007 (7.01) |
| A. thaliana leaf untreated | 80,329,562 | 35.59 | 74,144,556 | 58.16 | ||
| A. thaliana leaf 3 DAI with Fusarium | 95,285,902 | 36.88 | 91,697,050 | 57.79 | 606 (2.11) | 785 (2.74) |
| A. halleri mature pistils unpollinated | 106,156,558 | 36.88 | 75,012,556 | 73.92 | ||
| A. halleri pistils selfed 8 HAP | 93,961,972 | 36.71 | 67,574,404 | 72.59 | 173 (0.69) | 211 (0.84) |
| A. halleri pistils × A. lyrata pollen 8 HAP | 121,254,382 | 36.44 | 87,023,215 | 73.3 | 184 (0.73) | 197 (0.78) |
| A. halleri pistil 3 DAI with Fusarium | 83,771,668 | 36.68 | 56,172,094 | 66.81 | 1,724 (6.89) | 1,994 (7.97) |
| A. halleri leaf untreated | 127,526,910 | 36.42 | 89,168,588 | 65.78 | ||
| A. halleri leaf 3 DAI with Fusarium | 93,279,706 | 36.76 | 66,208,233 | 65.35 | 1,349 (5.39) | 517 (2.06) |
a
As a percentage of the total number of genes included in the reference genomes: A. thaliana TAIR10, 28,642 (including mitochondrial genes); A. halleri V1, 25,008 (including 68 chloroplast and mitochondrial genes). Genes expressed are those with RPKM ≥ 1.
b
For each species, nonpollinated pistils or untreated leaves were the points of reference for calculating differential expression. Differential expression is log2 fold change ≥ 2 for up-regulation or ≤ −2 for down-regulation, FDR-corrected P ≤ 0.0005. Values in parentheses are the number of genes differentially expressed, as a percentage of the total number of genes in each species.