Table 1.
Gene expression in wild type (WT) melon (Cucumis melo) and fefe roots. RNA-seq reads were mapped to cucumber transcripts (Cucumber Locus ID)
| Normalized Read Counts | |||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| logFC (−Fe/+Fe) | logFC (− Cu/+Cu) |
fefe | WT (Edisto) |
WT (snake) |
fefe | WT (Edisto) |
|||||||||||
| Melo n Gen e Nam e |
Cucumbe r Locus ID |
Top Arabidopsis thaliana Hit | fefe | WT (Ed ) |
WT (sn ) |
fefe | WT (Ed ) |
+F e |
− Fe |
+F e |
− Fe |
+F e |
− Fe |
+C u |
− Cu |
+C u |
− Cu |
| Ferric Reductase/oxidase family | |||||||||||||||||
| AT5G47910.1 RBOHD | |||||||||||||||||
| Csa3M84 5500.1 |
AT5G47910.1 RBOHD (RESPIRATORY BURST OXIDASE HOMOLOGUE D); NAD(P)H oxidase |
1.1 | 1.2 | 1.7 | 13 46 |
19 76 |
36 50 |
66 71 |
75 16 |
15 84 7 |
60 58 |
11 25 6 |
10 66 |
30 05 |
|||
| FRO 1 |
Csa5M17 5770.1 |
AT1G23020.1 FRO3; ferric- chelate reductase |
- 1.7 |
4.3 | 2.7 | - 5.0 |
- 3.3 |
50 0 |
15 4 |
41 0 |
80 58 |
29 1 |
18 13 |
17 37 |
44 | 11 47 |
12 3 |
| FRO 2 |
Csa3M18 3380.1 |
AT5G23980.1 FRO4 (FERRIC REDUCTION OXIDASE 4); ferric- chelate reductase |
- 2.1 |
- 2.6 |
3.8 | 2.6 | 28 61 |
66 3 |
10 04 |
16 78 |
10 5 |
17 | 20 1 |
24 24 |
18 94 |
93 37 |
|
| Csa1M42 3270.1 |
AT2G24520.1 AHA5 (Arabidopsis H(+)-ATPase 5); ATPase |
1.1 | 65 72 |
80 12 |
50 25 |
10 30 3 |
45 60 |
73 87 |
42 29 |
32 79 |
62 39 |
44 69 |
|||||
|
Metal
Transporters |
|||||||||||||||||
| Nra mp3 |
Csa2M42 3700.1 |
AT2G23150.1 NRAMP3 (NATURAL RESISTANCE- ASSOCIATED MACROPHAGE PROTEIN 3); inorganic anion transmembrane transporter/ manganese ion transmembrane transporter/ metal ion transmembrane transporter |
1.1 | 1.2 | 61 11 |
13 05 5 |
12 41 |
27 13 |
16 09 |
22 36 |
24 68 |
17 11 |
99 4 |
70 9 |
|||
| Nra mp1 |
Csa6M38 2880.1 |
AT1G80830.1 NRAMP1 (NATURAL RESISTANCE- ASSOCIATED MACROPHAGE PROTEIN 1); inorganic anion transmembrane transporter/ manganese ion transmembrane transporter/ metal ion transmembrane transporter |
3.7 | 1.7 | 17 4 |
84 | 77 5 |
97 03 |
16 88 |
54 38 |
16 7 |
89 | 30 78 |
12 80 |
|||
| IRT1 | Csa1M70 7110.1 |
AT4G19680.2 IRT2; iron ion transmembrane transporter/ zinc ion transmembrane transporter |
1.4 | - 2.5 |
38 6 |
24 8 |
42 8 |
11 17 |
24 6 |
47 3 |
80 1 |
12 8 |
61 4 |
39 5 |
|||
| IRT2 | Csa6M51 7980.1 |
AT4G19690.2 IRT1 (iron- regulated transporter 1); cadmium ion transmembrane transporter/ copper uptake transmembrane transporter/ iron ion transmembrane transporter/ manganese ion transmembrane transporter/ zinc ion transmembrane transporter |
3.0 | 12 | 10 3 |
3 | 4 | 6 | 9 | 1 | 1 | 2 | 1 | ||||
| ZIP2 | Csa7M16 2550.1 |
AT5G59520.1 ZIP2; copper ion transmembrane transporter/ transferase, transferring glycosyl groups / zinc ion transmembrane transporter |
1.3 | 2.2 | 14 0 |
72 | 54 | 46 | 78 | 81 | 42 | 85 | 43 | 17 0 |
|||
| ZIP5 | Csa4M61 8490.1 |
AT1G05300.1 ZIP5; cation transmembrane transporter/ metal ion transmembrane transporter |
- 1.0 |
83 | 81 | 40 2 |
45 7 |
17 3 |
16 2 |
25 | 31 | 14 0 |
55 | ||||
| COP T2 |
Csa1M52 6820.1 |
AT3G46900.1 COPT2; copper ion transmembrane transporter/ high affinity copper ion transmembrane transporter |
- 2.5 |
1.8 | - 1.6 |
1.4 | 1.7 | 27 8 |
49 | 57 | 19 4 |
47 | 15 | 87 | 18 4 |
17 9 |
51 5 |
| Csa3M69 6860.1 |
AT3G08040.1 FRD3 (FERRIC REDUCTASE DEFECTIVE 3); antiporter/ transporter |
- 3.9 |
- 2.4 |
65 | 50 | 3 | 19 | 17 9 |
12 | 20 | 3 | 6 | 14 | ||||
| Csa7M42 8170.1 |
AT3G08040.1 FRD3 (FERRIC REDUCTASE DEFECTIVE 3); antiporter/ transporter |
1.3 | 14 25 |
13 22 |
79 2 |
18 60 |
12 69 |
13 90 |
15 43 |
77 4 |
22 11 |
14 17 |
|||||
| Csa3M18 0310.1 |
AT4G23030.1 MATE efflux protein-related |
1.0 | 1.1 | 1.3 | 2.8 | 74 | 70 | 15 8 |
31 6 |
30 4 |
62 0 |
74 1 |
14 64 |
70 | 42 3 |
||
| Csa2M40 4760.1 |
AT1G65730.1 YSL7 (YELLOW STRIPE LIKE 7); oligopeptide transporter |
1.0 | 11 29 |
63 3 |
16 60 |
13 35 |
23 45 |
46 11 |
33 2 |
33 3 |
60 2 |
43 6 |
|||||
| Csa2M40 4780.1 |
AT1G48370.1 YSL8 (YELLOW STRIPE LIKE 8); oligopeptide transporter |
1.0 | 71 | 44 | 12 4 |
10 8 |
18 3 |
36 6 |
27 | 31 | 47 | 43 | |||||
| Csa3M23 8100.1 |
AT5G53550.1 YSL3 (YELLOW STRIPE LIKE 3); oligopeptide transporter |
- 1.2 |
1.1 | 1.7 | 41 6 |
28 9 |
15 5 |
11 4 |
31 8 |
14 0 |
14 9 |
27 2 |
14 4 |
40 4 |
|||
| Csa1M32 9900.1 |
AT5G53550.1 YSL3 (YELLOW STRIPE LIKE 3); oligopeptide transporter |
- 1.5 |
10 3 |
37 | 19 | 14 | 37 | 44 | 8 | 14 | 16 | 25 | |||||
| OPT 3 |
Csa1M18 0750.1 |
AT4G16370.1 ATOPT3 (OLIGOPEPTIDE TRANSPORTER); oligopeptide transporter |
2.1 | 32 99 |
14 59 2 |
45 7 |
87 2 |
48 4 |
74 2 |
14 48 |
74 0 |
20 1 |
24 1 |
||||
| Nicotianamine synthase family | |||||||||||||||||
| NAS 1 |
Csa2M03 4520.1 |
AT5G04950.1 NAS1 (NICOTIANAMINE SYNTHASE 1); nicotianamine synthase |
2.4 | 2.0 | - 2.7 |
50 1 |
27 31 |
21 | 86 | 17 | 9 | 16 6 |
22 | 42 | 18 | ||
| NAS 2 |
Csa1M42 3010.1 |
AT1G56430.1 NAS4 (NICOTIANAMINE SYNTHASE 4); nicotianamine synthase |
- 5.3 |
- 1.4 |
- 5.1 |
- 4.4 |
13 9 |
3 | 52 2 |
21 0 |
57 | 21 | 80 | 2 | 10 57 |
50 | |
| NAS 3 |
Csa2M03 4530.1 |
AT1G56430.1 NAS4 (NICOTIANAMINE SYNTHASE 4); nicotianamine synthase |
- 1.8 |
2.2 | - 3.5 |
- 3.2 |
15 0 |
44 | 27 1 |
12 15 |
60 2 |
46 9 |
32 4 |
23 | 52 0 |
54 | |
| NAS 4 |
Csa1M56 1410.1 |
AT1G56430.1 NAS4 (NICOTIANAMINE SYNTHASE 4); nicotianamine synthase |
- 2.2 |
- 3.3 |
- 1.7 |
16 9 |
81 | 75 | 39 | 80 | 17 | 92 | 8 | 54 | 14 | ||
| VIT1 family | |||||||||||||||||
| VIT1 | Csa5M55 0240.1 |
AT2G01770.1 VIT1 (vacuolar iron transporter 1); iron ion transmembrane transporter |
- 3.4 |
- 1.8 |
- 1.3 |
90 | 9 | 56 7 |
34 7 |
12 9 |
13 1 |
17 8 |
42 | 24 4 |
89 | ||
| NO DL1 |
Csa1M28 8020.1 |
AT4G30420.1 nodulin MtN21 family protein |
- 1.8 |
1.1 | 34 6 |
98 | 16 59 |
22 05 |
10 93 |
23 24 |
10 4 |
11 8 |
65 | 36 | |||
| NO DL2 |
Csa3M83 5770.1 |
AT5G40240.1 nodulin MtN21 family protein |
1.1 | 10 1 |
13 5 |
38 | 47 | 41 | 87 | 66 | 79 | 37 | 26 | ||||
| NO DL3 |
Csa6M41 1280.1 |
AT3G25190.1 nodulin, putative | - 4.6 |
- 1.8 |
- 1.4 |
- 1.0 |
62 | 3 | 29 5 |
80 | 12 4 |
68 | 15 3 |
48 | 92 8 |
39 2 |
|
| NO DL4 |
Csa7M32 5150.1 |
AT3G43660.1 nodulin, putative | - 2.7 |
- 1.3 |
35 | 5 | 37 | 27 | 27 | 11 | 31 | 24 | 64 | 64 | |||
|
Ferr
itin |
|||||||||||||||||
| Csa5M21 5130.1 |
AT2G40300.1 ATFER4 (ferritin 4); binding / ferric iron binding / oxidoreductase/ transition metal ion binding |
- 1.2 |
42 2 |
32 0 |
95 0 |
40 7 |
81 7 |
92 3 |
52 5 |
37 1 |
57 4 |
54 9 |
|||||
|
Transcription
factors |
|||||||||||||||||
| Csa1M07 4400.1 |
AT4G20970.1 basic helix-loop- helix (bHLH) family protein |
2.6 | 2.4 | 69 | 44 2 |
95 | 18 6 |
15 0 |
20 1 |
65 | 27 2 |
14 4 |
24 3 |
||||
| Csa1M58 9140.1 |
AT5G56960.1 basic helix-loop- helix (bHLH) family protein |
1.3 | 1.2 | 94 | 22 7 |
21 2 |
17 8 |
51 8 |
11 94 |
15 | 12 | 23 | 10 | ||||
| Csa2M19 3320.1 |
AT5G43650.1 basic helix-loop- helix (bHLH) family protein |
1.3 | 2.2 | 2.8 | 12 | 8 | 15 8 |
38 7 |
25 9 |
11 40 |
25 | 14 8 |
5 | 15 | |||
| Csa2M35 4790.1 |
AT4G33880.1 basic helix-loop- helix (bHLH) family protein/RSL2 |
4.9 | 4.5 | 10 | 2 | 2 | 57 | 1 | 23 | 6 | 0 | 3 | 1 | ||||
| Csa3M11 9500.1 |
AT1G01260.1 basic helix-loop- helix (bHLH) family protein |
1.0 | 1.3 | 62 7 |
67 6 |
13 42 |
24 32 |
15 69 |
30 72 |
15 73 |
22 62 |
42 6 |
91 4 |
||||
| Csa3M17 8580.1 |
AT5G51780.1 basix helix-loop- helix (bHLH) family protein |
2.0 | 37 | 25 | 10 | 14 | 39 | 15 5 |
1 | 1 | 1 | 0 | |||||
| Csa3M89 3390.1 |
AT5G65640.1 bHLH093 (beta HLH protein 93); DNA binding / transcription factor |
- 1.6 |
- 1.0 |
59 4 |
76 2 |
13 62 |
94 9 |
30 43 |
24 98 |
11 4 |
31 | 13 5 |
56 | ||||
| Csa4M64 2470.1 |
AT2G14760.1 basic helix-loop- helix protein / bHLH protein |
1.9 | 12 | 8 | 18 | 64 | 0 | 13 | 12 | 6 | 3 | 1 | |||||
| Csa5M42 0280.1 |
AT1G66470.1 basic helix-loop- helix (bHLH) family protein |
1.1 | 30 9 |
16 4 |
66 | 60 | 44 | 89 | 59 | 23 | 46 | 24 | |||||
| FIT | Csa6M14 8260.1 |
AT2G28160.1 FRU (FER-LIKE REGULATOR OF IRON UPTAKE); DNA binding / transcription factor |
1.9 | - 1.1 |
10 45 |
64 9 |
10 9 |
40 4 |
19 5 |
33 7 |
80 9 |
32 5 |
27 0 |
18 7 |
|||
| Csa6M49 7100.1 |
AT2G22750.2 basic helix-loop- helix (bHLH) family protein |
1.6 | 5 | 4 | 39 | 73 | 14 2 |
42 6 |
5 | 18 | 2 | 1 | |||||
| Csa6M49 7110.1 |
AT4G37850.1 basic helix-loop- helix (bHLH) family protein |
1.8 | 3.1 | 2.2 | 68 | 30 | 71 6 |
86 5 |
42 8 |
14 13 |
10 8 |
80 1 |
21 | 80 | |||
| Csa6M49 7120.1 |
AT4G37850.1 basic helix-loop- helix (bHLH) family protein |
30 | 16 | 5 | 4 | 3 | 11 | 6 | 7 | 5 | 7 | ||||||
| Csa3M116 720.1 |
AT2G44840.1 ERF13 (ETHYLENE-RESPONSIVE ELEMENT BINDING FACTOR 13); DNA binding / transcription factor |
2.4 | 2.7 | 3.8 | 6 | 2 | 91 | 23 1 |
12 0 |
60 3 |
67 | 34 5 |
3 | 32 | |||
| Csa3M11 6730.1 |
AT2G44840.1 ERF13 (ETHYLENE-RESPONSIVE ELEMENT BINDING FACTOR 13); DNA binding / transcription factor |
2.3 | 2.1 | 4 | 2 | 31 | 58 | 35 | 16 4 |
42 | 14 5 |
2 | 15 | ||||
| Csa5M15 5570.1 |
AT1G12610.1 DDF1 (DWARF AND DELAYED FLOWERING 1); DNA binding / sequence-specific DNA binding / transcription factor |
1.0 | 2.0 | 5.0 | 2 | 2 | 29 2 |
57 5 |
32 8 |
34 0 |
20 1 |
69 3 |
2 | 68 | |||
| Csa7M16 9070.1 |
AT4G39250.1 ATRL1 (ARABIDOPSIS RAD-LIKE 1); DNA binding / transcription factor |
5.0 | - 6.3 |
1 | 1 | 2 | 66 | 10 | 13 | 1 | 0 | 25 | 0 | ||||
| Csa3M18 0260.1 |
AT4G25490.1 CBF1 (C- REPEAT/DRE BINDING FACTOR 1); DNA binding / transcription activator/ transcription factor |
- 1.6 |
1.1 | 1.0 | 3.6 | 30 | 9 | 81 | 16 8 |
15 3 |
14 7 |
18 55 |
30 44 |
10 2 |
10 60 |
||
| Csa3M71 0870.1 |
AT1G80840.1 WRKY40; transcription factor |
1.3 | 1.2 | 3.4 | 25 5 |
17 9 |
12 44 |
25 45 |
23 33 |
57 75 |
31 29 |
58 44 |
24 8 |
23 03 |
|||
| Csa7M07 3700.1 |
AT4G34410.1 RRTF1 ({REDOX RESPONSIVE TRANSCRIPTION FACTOR 1); DNA binding / transcription factor |
1.4 | 2.1 | 1.6 | 4.1 | 2 | 2 | 19 | 47 | 21 | 90 | 26 9 |
67 0 |
9 | 13 6 |
||
| Csa2M29 7760.1 |
AT5G50080.1 DNA binding / transcription factor |
1.5 | 1.2 | 15 0 |
96 | 24 9 |
68 8 |
16 9 |
38 3 |
71 | 32 | 86 | 52 | ||||
| Csa3M40 5510.1 |
AT5G48150.1 PAT1 (phytochrome a signal transduction 1); signal transducer/ transcription factor |
1.3 | 1.5 | 3.6 | 24 8 |
26 4 |
55 8 |
13 49 |
14 42 |
39 93 |
46 08 |
74 12 |
28 1 |
31 95 |
|||
| Csa6M42 5790.1 |
AT3G44260.1 CCR4-NOT transcription complex protein, putative |
1.3 | 1.6 | 3.0 | 65 | 57 | 26 9 |
29 5 |
10 24 |
24 43 |
10 30 |
26 23 |
10 4 |
70 1 |
|||
Significant log fold-change (logFC) is shown for fefe, Edisto (Ed) and snake melon (sn) for Fe treatments, and for Edisto and fefe for Cu treatments. Normalized read counts for each transcript are also shown.