Table 1.
Differential expression and methylation of CYCLIN (CYC) and MADS-box genes in Kiwifruit bud samples between August and June. CYC genes are indicated in blue font and MADS box genes in red font. Kiwifruit FLC-like associated with epigenetic regulation by histone modifications and long non-coding RNAs is indicated by an asterisk.
| Annotation | DESeq analysis | |||||
|---|---|---|---|---|---|---|
| Gene_id | TAIR top hit | e value | log2fold change | padj | meth.diff. (August) | Category (DEG_DMR) |
| Acc00557 | AT5G67260 | CYCD3;2 | 9.5E-80 | 1.50 | 2.32E-03 | −34.45 | UP_HYPO |
| Acc01102 | AT1G20610 | CYCB2;3 | 2.6E-152 | 9.31 | 7.13E-37 | −38.80 | UP_HYPO |
| Acc01195 | AT5G65420 | CYCD4;1 | 2E-90 | 2.60 | 7.61E-09 | −40.91 | UP_HYPO |
| Acc04491 | AT1G76310 | CYCB2;4 | 0 | 7.51 | 7.07E-46 | −38.12 | UP_HYPO |
| Acc04754 | AT4G34160 | CYCD3;1 | 1.8E-101 | 3.20 | 5.10E-61 | −36.11 | UP_HYPO |
| Acc04763 | AT1G47210 | CYCA3;2 | 3.1E-150 | 9.28 | 1.71E-14 | −41.36 | UP_HYPO |
| Acc04782 | AT4G37630 | CYCD5;1 | 1.5E-45 | 2.32 | 2.20E-33 | −39.08 | UP_HYPO |
| Acc06013 | AT4G34160 | CYCD3;1 | 6.3E-95 | 7.05 | 5.09E-11 | −36.76 | UP_HYPO |
| Acc06877 | AT1G70210 | CYCD1;1 | 4.5E-63 | 2.01 | 7.82E-22 | −38.73 | UP_HYPO |
| Acc10304 | AT5G67260 | CYCD3;2 | 4.1E-93 | 3.36 | 2.25E-40 | −28.12 | UP_HYPO |
| Acc10528 | AT5G65420 | CYCD4;1 | 1.2E-92 | 2.12 | 1.81E-25 | −35.62 | UP_HYPO |
| Acc10862 | AT1G76310 | CYCB2;4 | 1.5E-155 | 7.28 | 3.72E-43 | −41.52 | UP_HYPO |
| Acc11766 | AT4G34160 | CYCD3;1 | 1.2E-101 | 1.53 | 2.80E-82 | −36.59 | UP_HYPO |
| Acc11958 | AT1G20610 | CYCB2;3 | 0 | 2.66 | 1.20E-19 | −36.98 | UP_HYPO |
| Acc12063 | AT4G34160 | CYCD3;1 | 6.5E-100 | 1.51 | 3.44E-44 | −30.66 | UP_HYPO |
| Acc12069 | AT1G47230 | CYCA3;4 | 7.1E-156 | 5.53 | 1.02E-57 | −40.81 | UP_HYPO |
| Acc12153 | AT5G65420 | CYCD4;1 | 1.4E-83 | 1.96 | 4.79E-32 | −36.77 | UP_HYPO |
| Acc12296 | AT1G44110 | CYCA1;1 | 0 | 8.17 | 5.52E-35 | −34.95 | UP_HYPO |
| Acc12588 | AT1G80370 | CYCA2;4 | 1.5E-172 | 1.56 | 9.44E-12 | −41.56 | UP_HYPO |
| Acc13238 | AT5G06150 |CYCB1;2 | 1.6E-161 | 10.15 | 3.54E-33 | −34.79 | UP_HYPO |
| Acc13514 | AT4G03270 | CYCD6;1 | 7.09E-28 | 1.33 | 3.90E-08 | −36.89 | UP_HYPO |
| Acc14887 | AT1G16330 | CYCB3;1 | 4.7E-150 | 1.33 | 3.44E-38 | −33.07 | UP_HYPO |
| Acc17841 | AT1G80370 | CYCA2;4 | 4.4E-172 | 2.07 | 9.10E-29 | −37.22 | UP_HYPO |
| Acc20604 | AT4G03270 | CYCD6;1 | 2.7E-65 | 1.71 | 6.60E-04 | −38.88 | UP_HYPO |
| Acc21080 | AT1G47230 | CYCA3;4 | 9.5E-133 | 3.01 | 6.82E-14 | −39.14 | UP_HYPO |
| Acc21097 | AT5G67260 | CYCD3;2 | 1.2E-80 | 1.74 | 2.39E-53 | −40.50 | UP_HYPO |
| Acc22522 | AT5G11300 |CYCA2;2 | 1.3E-156 | 5.19 | 6.6E-121 | −33.58 | UP_HYPO |
| Acc23082 | AT3G11520 | CYCB1;3 | 1.4E-161 | 8.56 | 7.52E-61 | −33.07 | UP_HYPO |
| Acc23489 | AT1G76310 | CYCB2;4 | 0 | 10.25 | 1.58E-17 | −39.60 | UP_HYPO |
| Acc23775 | AT4G34160 | CYCD3;1 | 2.9E-102 | 5.36 | 2.68E-96 | −26.64 | UP_HYPO |
| Acc23788 | AT1G47210 | CYCA3;2 | 1.7E-149 | 8.83 | 3.58E-13 | −37.15 | UP_HYPO |
| Acc23807 | AT4G37630 | CYCD5;1 | 3.1E-46 | 3.89 | 3.43E-49 | −34.52 | UP_HYPO |
| Acc23897 | AT5G65420 | CYCD4;1 | 2.6E-84 | 1.32 | 1.44E-08 | −36.68 | UP_HYPO |
| Acc25062 | AT4G03270 | CYCD6;1 | 3.4E-62 | 1.67 | 9.63E-13 | −36.04 | UP_HYPO |
| Acc30317 | AT5G06150 |CYCB1;2 | 3.9E-149 | 9.94 | 4.89E-42 | −31.10 | UP_HYPO |
| Acc30987 | AT5G67260 | CYCD3;2 | 1.4E-104 | 5.04 | 2.62E-59 | −42.87 | UP_HYPO |
| Acc32381 | AT2G26760 | CYCB1;4 | 6.5E-144 | 10.21 | 8.31E-23 | −34.36 | UP_HYPO |
| Acc01045 | AT3G54340 | AP3 | 2.3E-73 | 2.64 | 1.67E-95 | −35.86 | UP_HYPO |
| Acc02284 | AT1G69120 | AP1 | 2.09E-88 | 8.03 | 2.96E-14 | −32.63 | UP_HYPO |
| Acc02285 | AT3G02310 | SEP2 | 2.3E-106 | 8.05 | 2.44E-14 | −36.34 | UP_HYPO |
| Acc04040 | AT5G60910 |FUL | 1.9E-90 | 8.15 | 1.06E-14 | −32.92 | UP_HYPO |
| Acc04041 | AT3G02310 | SEP2 | 6.3E-109 | 3.01 | 5.46E-38 | −32.80 | UP_HYPO |
| Acc05042 | AT5G20240 | PI | 1.04E-89 | 8.28 | 2.83E-11 | −29.28 | UP_HYPO |
| Acc06158 | AT1G24260 | SEP3 | 6E-122 | 7.96 | 2.56E-10 | −41.45 | UP_HYPO |
| Acc07652 | AT2G45660 |SOC1 | 3E-86 | 1.71 | 3.96E-77 | −35.09 | UP_HYPO |
| Acc08270 | AT1G24260 | SEP3 | 9.5E-121 | 10.32 | 1.42E-17 | −32.24 | UP_HYPO |
| Acc09079 | AT2G45650 | AGL6 | 5.7E-100 | 6.62 | 6.29E-14 | −38.61 | UP_HYPO |
| Acc10416 | AT3G54340 | AP3 | 1.01E-23 | 3.50 | 3.33E-04 | −35.32 | UP_HYPO |
| Acc10522 | AT2G22540 | SVP | 6.5E-113 | 1.81 | 4.63E-47 | −36.88 | UP_HYPO |
| Acc14105 | AT1G69120 | AP1 | 1.5E-95 | 10.34 | 1.13E-17 | −39.60 | UP_HYPO |
| Acc14300 | AT1G24260 | SEP3 | 9.9E-123 | 8.71 | 1.75E-12 | −39.32 | UP_HYPO |
| Acc14601 | AT2G45650 | AGL6 | 3.4E-106 | 9.14 | 7.03E-14 | −35.05 | UP_HYPO |
| Acc16642 | AT2G45660 | SOC1 | 5.1E-42 | 2.24 | 3.56E-39 | −33.75 | UP_HYPO |
| Acc18368 | AT5G60910 | FUL | 1.1E-106 | 3.28 | 5.3E-252 | −39.91 | UP_HYPO |
| Acc20728 | AT4G18960 | AG | 9.2E-123 | 7.89 | 3.23E-10 | −35.76 | UP_HYPO |
| Acc21883 | AT5G15800 | SEP1 | 4.9E-97 | 10.56 | 1.99E-18 | −36.90 | UP_HYPO |
| Acc22088 | AT3G58780 | SHP1 | 7.3E-46 | 8.12 | 7.53E-11 | −36.09 | UP_HYPO |
| Acc23601 | AT3G54340 | AP3 | 2.7E-93 | 5.87 | 5.81E-20 | −34.75 | UP_HYPO |
| Acc24088 | AT5G20240 | PI | 1.06E-86 | 6.64 | 6.58E-07 | −36.47 | UP_HYPO |
| Acc26639 | AT5G60910 |FUL | 1.7E-94 | 9.42 | 1.86E-19 | −34.02 | UP_HYPO |
| Acc26640 | AT3G02310 | SEP2 | 2.1E-103 | 8.92 | 3.52E-13 | −34.32 | UP_HYPO |
| Acc27997 | AT2G45650 | AGL6 | 2.5E-43 | 7.80 | 1.49E-19 | −32.69 | UP_HYPO |
| Acc29300 | AT3G02310 | SEP2 | 1.03E-98 | 9.43 | 9.46E-15 | −39.66 | UP_HYPO |
| Acc32725 | AT1G24260 | SEP3 | 7.3E-124 | 10.26 | 1.94E-17 | −38.30 | UP_HYPO |
| Acc32983 | AT1G26310 | CAL | 3.6E-55 | 5.10 | 1.40E-23 | −35.78 | UP_HYPO |
| Acc01231 | AT1G22130 | AGL104 | 2.2E-30 | −1.26 | 1.79E-22 | −33.92 | DOWN_HYPO |
| Acc05562* | AT5G65070 | MAF4 | 8E-39 | −3.53 | 0.00E + 00 | −31.98 | DOWN_HYPO |
| Acc06844 | AT3G57230 | AGL16 | 6.5E-93 | −1.99 | 3.24E-19 | −39.00 | DOWN_HYPO |
| Acc07718 | AT5G48670 |AGL80 | 3.4E-39 | −1.55 | 9.78E-05 | −35.51 | DOWN_HYPO |
| Acc08919 | AT1G18750 | AGL65 | 1.9E-50 | −1.56 | 9.99E-29 | −35.20 | DOWN_HYPO |
| Acc12070 | AT1G77980 | AGL66 | 4.2E-50 | −2.13 | 1.96E-23 | −38.08 | DOWN_HYPO |
| Acc15737 | AT2G45660 |SOC1 | 2.3E-76 | −1.85 | 4.40E-91 | −37.25 | DOWN_HYPO |
| Acc24142 | AT1G71692 | XAL1 | 3.06E-78 | −1.75 | 1.62E-32 | −28.96 | DOWN_HYPO |