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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)

From: Low-temperature-induced changes in the transcriptome reveal a major role of CgSVP genes in regulating flowering of Cymbidium goeringii

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]