Table 3.
Differentially expressed genes related to floral development. Fold change = log2(expression value of each gene after cold treatment/before cold treatment), expression value = RPKM [total exon reads / mapped reads (millions)] × exon length (kb)
| Locus | Ck | Cold | log2(fold_change) | p_value | Description |
|---|---|---|---|---|---|
| MADS-box gene | |||||
| CL8764Contig1 | 9.8869 | 0.4959 | −4.3174 | 9.43E-05 | SOC1 [Dendrobium hybrid cultivar] |
| CL8650Contig1 | 20.9806 | 1.0767 | −4.2844 | 6.47E-05 | SOC1 [Dendrobium hybrid cultivar] |
| ep123.comp43097 | 0.4641 | 6.4672 | 2.4787 | 2.03E-02 | SOC1 [Dendrobium hybrid cultivar] |
| ep456.comp50389 | 4.099 | 71.4805 | 4.1242 | 8.95E-05 | SOC1-like protein [Prunus x yedoensis] |
| ep123.comp44547 | 14.9139 | 2.9644 | −2.3308 | 6.67E-61 | SVP1 [Actinidia deliciosa] |
| ep456.comp28009 | 114.453 | 5.2832 | −4.4372 | 0.00E+ 00 | MADS-box protein SVP [Arabidopsis thaliana] |
| ep456.comp36141 | 42.2288 | 8.5568 | −2.3031 | 4.71E-190 | PREDICTED: MADS-box protein SVP [Vitis vinifera] |
| ep456.comp38228 | 13.3352 | 0.8606 | −3.9538 | 5.00E-04 | FRUITFULL-like MADS box protein 1 [Dendrobium thyrsiflorum] |
| ep456.comp717274 | 15.2507 | 232.579 | 3.9308 | 1.61E-04 | AP1-like MADS-box protein [Cymbidium ensifolium] |
| CL551Contig1 | 0.0892 | 5.9554 | 6.0604 | 1.87E-06 | AGL66 protein [Eschscholzia californica] |
| ep123.comp36586 | 10.2183 | 136.628 | 3.741 | 3.16E-04 | AP3 [Cymbidium goeringii] |
| ep456.comp49009 | 0.2395 | 6.6177 | 4.7883 | 2.00E-04 | AP3 [Cymbidium goeringii] |
| Other flowering and floral related gene | |||||
| ep123.comp38616 | 3.0342 | 0.5423 | −1.9762 | 9.43E-05 | Flowering locus T protein [Ananas comosus] |
| ep456.comp59699 | 0.8817 | 0.2078 | −2.0139 | 5.00E-04 | Flowering locus D [Zea mays] |
| ep123.comp42797 | 1.0459 | 41.3741 | 5.306 | 6.47E-05 | AP2–7 [Erycina pusilla] |
| ep123.comp218062 | 26.5682 | 0.7566 | −5.134 | 2.03E-02 | LEAFY [Cymbidium hybrid cultivar] |
| ep123.comp738577 | 40.6535 | 1.3573 | −4.9045 | 8.95E-05 | LEAFY, partial [Cattleya hybrid cultivar] |
| ep456.comp48048 | 9.3535 | 380.927 | 5.3479 | 6.67E-61 | PREDICTED: late embryogenesis abundant protein D-29-like [Solanum lycopersicum] |
| ep123.comp19364 | 3.8409 | 89.0779 | 4.5356 | 0.00E+ 00 | PREDICTED: late embryogenesis abundant protein D-34-like [Cicer arietinum] |
| CL4811Contig1 | 0.0451 | 5.3112 | 6.8811 | 4.71E-190 | Putative aquaporin TIP5–1 [Aegilops tauschii] |
| CL3697Contig1 | 1.4658 | 44.228 | 4.9152 | 5.00E-04 | PREDICTED: 18 kDa seed maturation protein-like [Cucumis sativus] |
| Plant hormone signaling pathway | |||||
| CL8703Contig1 | 4.2816 | 0.1327 | −5.0116 | 9.43E-05 | PREDICTED: DELLA protein RGL2 [Vitis vinifera] |
| CL9507Contig1 | 84.2097 | 4.8002 | −4.1328 | 5.00E-04 | PREDICTED: auxin-induced protein 15A-like [Glycine max] |
| ep456.comp45207 | 0.1394 | 14.8622 | 6.736 | 6.47E-05 | SAUR11 - auxin-responsive SAUR family member [Zea mays] |
| ep456.comp58943_c0_seq9:0–1130 | 0.2642 | 690.516 | 11.3521 | 2.03E-02 | ABA related CCAAT-box binding factor HAP5 homolog [Daucus carota] |
| ep123.comp22898 | 0.4163 | 25.9618 | 5.9625 | 8.95E-05 | PREDICTED: ABA related transcription factor GTE1-like [Vitis vinifera] |
| Temperature-responsive factors | |||||
| ep456.comp328221 | 16.1755 | 6.2463 | 0.0003 | 9.43E-05 | CBF-like transcription factor [Trachycarpus fortunei] |
| ep123.comp36229 | 7.1138 | −6.1581 | 0 | 5.00E-04 | Chaperone [Agave tequilana] |
| ep123.comp38271 | 8.8938 | −4.5248 | 0 | 6.47E-05 | Chaperone [Agave tequilana] |
| ep456.comp54221 | 11.8107 | −3.6707 | 0.0004 | 2.03E-02 | Chaperone [Agave tequilana] |
| CL5833Contig1 | 3.8015 | −4.1095 | 0.0001 | 8.95E-05 | Chloroplast small heat shock protein [Agave americana] |
| ep123.comp38941 | 3.8102 | −6.1497 | 0 | 6.67E-61 | Class-1 LMW heat shock protein [Ananas comosus] |
| ep456.comp63219 | 89.7919 | −4.358 | 0.0001 | 4.71E-190 | Class-1 LMW heat shock protein [Ananas comosus] |
| CL8847Contig1 | 18.538 | −3.6826 | 0.0004 | 5.00E-04 | Mitochondrial small heat shock protein [Capsicum annuum] |
| ep123.comp39275 | 8.2354 | −3.6881 | 0.0004 | 1.61E-04 | PREDICTED: 17.4 kDa class III heat shock protein-like [Glycine max] |
| CL276Contig2 | 8.1857 | −4.9339 | 0 | 1.87E-06 | PREDICTED: 17.9 kDa class I heat shock protein-like [Brachypodium distachyon] |
| Other transcription factors | |||||
| ep456.comp51260 | 0.2133 | 208.395 | 9.9324 | 9.43E-05 | PREDICTED: WRKY transcription factor 6-like [Vitis vinifera] |
| ep123.comp34195 | 38.4439 | 2.4205 | −3.9894 | 5.00E-04 | PREDICTED: WRKY transcription factor 22 [Vitis vinifera] |
| ep123.comp25957 | 50.8577 | 3.9329 | −3.6928 | 6.47E-05 | Putative MYB DNA-binding domain superfamily protein [Zea mays] |
| ep456.comp42603 | 3.1925 | 364.995 | 6.837 | 2.03E-02 | Putative R2R3-MYB transcription factor [Citrus sinensis] |
| CL10849Contig1 | 0.0499 | 9.6423 | 7.5943 | 8.95E-05 | TPA: putative MYB DNA-binding domain superfamily protein [Zea mays] |
| ep123.comp101748 | 11.1484 | 0.3893 | −4.8396 | 6.67E-61 | TPA: putative HLH DNA-binding domain superfamily protein [Zea mays] |
| CL2976Contig1 | 17.7943 | 0.9644 | −4.2057 | 0.00E+ 00 | Putative bHLH transcription factor [Arabidopsis thaliana] |
| ep456.comp28555 | 7.4971 | −6.2209 | 0 | 4.71E-190 | CYP86C1 [Arabidopsis lyrata subsp. lyrata] |