SUPPLEMENTAL TABLES: Summary of BLAST results of genes isolated from the
various cold and photoperiod subtractions.

Table 1^z^. Peach Genes Down-regulated at 5 °C in NB/LD^y^ \[AF
subtraction\].

+---+----------------------+------+--------------------+------+------+
| N | Gene Match           | A    | Function           | Hig  | E    |
| o | Description \[Source | cces |                    | hest | V    |
| . | organism\]           | sion |                    | S    | alue |
| o |                      | Nu   |                    | core |      |
| f |                      | mber |                    | \[Bi | \[   |
| C |                      |      |                    | ts\] | Lowe |
| l |                      |      |                    |      | st\] |
| o |                      |      |                    |      |      |
| n |                      |      |                    |      |      |
| e |                      |      |                    |      |      |
| s |                      |      |                    |      |      |
+---+----------------------+------+--------------------+------+------+
| 1 | Thioredoxin          | AAM6 | Redox regulation   | 77   | 8    |
|   | \[*Arabidopsi        | 1520 | of protein         |      | e-14 |
|   | thaliana*\]          |      | activity and       |      |      |
|   |                      |      | signaling; nearly  |      |      |
|   |                      |      | identical to       |      |      |
|   |                      |      | At3g06730          |      |      |
+---+----------------------+------+--------------------+------+------+
| 2 | Fructose             | T1   | Glycolysis         | 233  | 2    |
|   | bisphosphate         | 2416 |                    |      | e-60 |
|   | aldolase             |      |                    |      |      |
|   | \[*Mesembryanthemum  |      |                    |      |      |
|   | crystallinum*\]      |      |                    |      |      |
+---+----------------------+------+--------------------+------+------+
| 1 | 50S Ribosomal        | N    | Chloroplast        | 65   | 6    |
|   | protein              | P_86 | encoded protein    |      | e-10 |
|   | \[*Calycanthus       | 2777 | L20 (*rpl20*);     |      |      |
|   | florida*\]           |      | organelle          |      |      |
|   |                      |      | translation        |      |      |
+---+----------------------+------+--------------------+------+------+
| 1 | Transl               | O0   | Binds calcium and  | 162  | 1    |
|   | ationally-controlled | 3992 | stabilizes         |      | e-39 |
|   | tumor protein        |      | microtubules;      |      |      |
|   | \[*Fragaria x        |      | associated with    |      |      |
|   | ananassa*\]          |      | regulation of cell |      |      |
|   |                      |      | division           |      |      |
+---+----------------------+------+--------------------+------+------+
| 1 | Acetohydroxy acid    | CAB6 | Ilv/Val synthesis  | 274  | 3    |
|   | isomeroreductase     | 1890 |                    |      | e-73 |
|   | \[*Pisum sativum*\]  |      |                    |      |      |
+---+----------------------+------+--------------------+------+------+
| 1 | Putative splicing    | N    | RNA processing; U2 | 112  | 5    |
|   | factor \[*A.         | P_19 | snRNP auxiliary    |      | e-24 |
|   | thaliana*\]          | 9096 | factor; At5g42820  |      |      |
+---+----------------------+------+--------------------+------+------+
| 2 | Expressed^x^ protein | N    | note:several       | 95   | 7    |
|   | \[*A. thaliana*\]    | P_56 | frames seem to     |      | e-19 |
|   |                      | 7555 | work in BLAST      |      |      |
|   |                      |      |                    |      |      |
|   |                      |      | At4g18400          |      |      |
+---+----------------------+------+--------------------+------+------+
| 2 | Cytosolic ascorbate  | AAD4 | Oxidative stress   | 325  | 7    |
|   | peroxidase           | 1407 | responses          |      | e-88 |
|   | \[*Fragaria x        |      |                    |      |      |
|   | ananassa*\]          |      |                    |      |      |
+---+----------------------+------+--------------------+------+------+
| 1 | PSI P700 apoprotein  | N    | Photosynthesis     | 150  | 2    |
|   | A2 \[*Calycanthus    | P_86 |                    |      | e-43 |
|   | fertilis*\]          | 2753 |                    |      |      |
+---+----------------------+------+--------------------+------+------+
| 1 | Hypothetical^x^      | BX81 | At1g69230          | 60   | 3e-6 |
|   | protein \[*A.        | 7727 | (BLASTn); putative |      |      |
|   | thaliana*\]          |      | ni                 |      |      |
|   |                      |      | trilase-associated |      |      |
|   |                      |      | protein            |      |      |
+---+----------------------+------+--------------------+------+------+

^z^Results are based on the BLASTx, tBLASTx and BLASTn databases at
NCBI. A Threshold of 1.00 was used and each alignment was visually
inspected for similarity matches. Additional information was obtained
from Clustal W analyses of similar or related sequences at the European
Molecular Biology Laborotory, the Conserved Domain Database at the
National Center for Biotechnology Information), the 6-Frame Translator
at the Baylor College of Medicine Search Launcher and the PROSITE
program at ExPASy. Vector and adaptor sequences were removed after
alignment in VecScreen (NCBI). Number of clones: more than 1 indicates
that identical clones were obtained; if different alleles or families
were observed, they are treated as individual clones.

^y^NB = Night Break (16 h light/ 8 h dark with a 15 min light
interruption 4 h after the start of the dark period)

LD = Long Days (16 h light/ 8 h dark)

SD = Shor Days (8 h light/ 16 h dark)

^x^Unknown = no matches in the BLAST databases

Hypothetical = identified from genomic sequence by bioinformatic
programs

Expressed = identified from genomic sequence, but found in ESTs or cDNA
populations

Unknown sequences were clustered at the CAP sequence assembly machine at
the Istituto FIRC Di Oncologia Molecolare to identify individual gene
sequences.

Table 2. Peach Genes Up-regulated at 5 °C in LD/NB \[AR subtraction\].

+-----+---------------------+------+--------------------+------+------+
| No. | Gene Match          | A    | Function           | Hig  | E    |
| of  | Description         | cces |                    | hest | V    |
|     | \[Source organism\] | sion |                    | S    | alue |
| Clo |                     |      |                    | core |      |
| nes |                     | Nu   |                    | \[Bi | \[   |
|     |                     | mber |                    | ts\] | Lowe |
|     |                     |      |                    |      | st\] |
+-----+---------------------+------+--------------------+------+------+
| 5   | Expressed protein   | N    | Contains weak      | 281  | 5    |
|     |                     | M_11 | similarity to      |      | e-75 |
|     |                     | 6078 | isopenicillin N    |      |      |
|     |                     |      | epimerase from     |      |      |
|     |                     |      | *Streptomyces      |      |      |
|     |                     |      | clavuligerus,*     |      |      |
|     |                     |      | At3g62130          |      |      |
+-----+---------------------+------+--------------------+------+------+
| 1   | Rubber elongation   | N    | Allergenic to      | 171  | 1    |
|     | factor related      | M-10 | people with spina  |      | e-41 |
|     | protein             | 5404 | bifida; otherwise, |      |      |
|     | \[*Arabidopsis      |      | not a major        |      |      |
|     | thaliana*\]         |      | allergen;          |      |      |
|     |                     |      | At1g67360          |      |      |
+-----+---------------------+------+--------------------+------+------+
| 2   | -1,3 glucanase     | AY17 | Stress related;    | 84   | 4    |
|     | \[*Fragaria* *x*    | 0375 | cell wall          |      | e-16 |
| 1   | *ananassa*\]        |      | metabolism         | 60   |      |
|     |                     | AF14 |                    |      | 2e-8 |
|     | \[*Nicotiana        | 1653 |                    |      |      |
|     | tabacum*\]          |      |                    |      |      |
+-----+---------------------+------+--------------------+------+------+
| 4   | ORF2, similar to    | 1308 | {not the same as   | 59   | 4e-8 |
|     | soybean nodulin     | 219B | the organ-specific |      |      |
|     | \[*Glycine max*\]   |      | protein gene}      |      |      |
+-----+---------------------+------+--------------------+------+------+
| 1   | Dehydrin \[*Prunus  | AF20 | *Ppdhn3*; Little   | 105  | 2    |
|     | dulcis*\]           | 9908 | similarity to      |      | e-21 |
|     |                     |      | *Ppdhn1* or *2*    |      |      |
+-----+---------------------+------+--------------------+------+------+
| 2   | Class IV Chitinase, | N    | Probably           | 183  | 2    |
|     | family 19 \[*A.     | M_11 | stress/pathogen    |      | e-45 |
|     | thaliana*\]         | 5302 | responsive;        |      |      |
|     |                     |      | At3g54420          |      |      |
+-----+---------------------+------+--------------------+------+------+
| 1   | Phase-change        | AJ27 | Developmentally    | 56   | 8e-5 |
|     | protein \[*Quercus  | 1778 | regulated; BLASTn  |      |      |
|     | robur*\]            |      |                    |      |      |
+-----+---------------------+------+--------------------+------+------+
| 1   | 60S Ribosomal       | AF30 | Translation; L17A  | 159  | 1    |
|     | Protein \[*Petunia  | 7336 | & B in *A.         |      | e-38 |
|     | hybrida*\]          |      | thaliana*          |      |      |
+-----+---------------------+------+--------------------+------+------+
| 2   | Hypothetical        | AF32 | At5g17460          | 114  | 1    |
|     | protein \[*A.       | 4993 |                    |      | e-24 |
| 1   | thaliana*\]         |      | Has PQ loop domain | 387  |      |
|     |                     | AY04 | and other repeats; |      | 1e   |
| 1   | Hypothetical        | 6029 | At4g36850          | 121  | -106 |
|     | protein \[*A.       |      |                    |      |      |
|     | thaliana*\]         | AY08 | Has TRAF/MATH      |      | 1    |
|     |                     | 5057 | domain; some       |      | e-26 |
|     | Hypothetical        |      | similarity to      |      |      |
|     | protein \[*A.       |      | ubiquitin protease |      |      |
|     | thaliana*\]         |      | 12; At3g17380      |      |      |
+-----+---------------------+------+--------------------+------+------+
| 1   | Glyceraldehyde 3    | AJ24 | Glycolysis;        | 348  | 6    |
|     | Phosphate           | 6011 | chloroplastic      |      | e-95 |
|     | Dehydrogenase       |      |                    |      |      |
|     | \[*Capsicum         |      |                    |      |      |
|     | annuum*\]           |      |                    |      |      |
+-----+---------------------+------+--------------------+------+------+
| 4   | Thaumatin \[*Prunus | P8   | Defense; PR gene;  | 485  | 1e   |
|     | persica*\]          | 3335 | *PpAZ8*            |      | -136 |
| 2   |                     |      |                    |      |      |
|     | same                | P8   | *PpAZ4*            |      |      |
|     |                     | 3332 |                    |      |      |
+-----+---------------------+------+--------------------+------+------+
| 11  | Unknown^x^          |      | Group 1            |      |      |
|     |                     |      |                    |      |      |
| 1   |                     |      | Group 2 (Very      |      |      |
|     |                     |      | pro-rich in best   |      |      |
| 1   |                     |      | translation frame) |      |      |
|     |                     |      |                    |      |      |
| 1   |                     |      | Group 3            |      |      |
|     |                     |      |                    |      |      |
| 3   |                     |      | Group 4            |      |      |
|     |                     |      |                    |      |      |
| 1   |                     |      | Group 5            |      |      |
|     |                     |      |                    |      |      |
| 1   |                     |      | Group 6            |      |      |
|     |                     |      |                    |      |      |
|     |                     |      | Group 7            |      |      |
+-----+---------------------+------+--------------------+------+------+
| 1   | Ubiquitin precursor | S2   | Protein            | 199  | 1    |
|     | \[*Helianthus       | 5164 | degradation        |      | e-50 |
|     | annuus*\]           |      |                    |      |      |
+-----+---------------------+------+--------------------+------+------+

Table 3. Peach Genes Down-regulated in SD at 25 °C \[BF subtraction\].

+----+---------------------+------+--------------------+------+------+
| N  | Gene Match          | A    | Function           | Hig  | E    |
| o. | Description         | cces |                    | hest | V    |
| of | \[Source organism\] | sion |                    | S    | alue |
| Cl |                     | Nu   |                    | core |      |
| on |                     | mber |                    | \[Bi | \[   |
| es |                     |      |                    | ts\] | Lowe |
|    |                     |      |                    |      | st\] |
+----+---------------------+------+--------------------+------+------+
| 2  | Unknown             |      | Group 8            |      |      |
|    |                     |      |                    |      |      |
| 2  |                     |      | Group 9            |      |      |
|    |                     |      |                    |      |      |
| 1  |                     |      | Group 10           |      |      |
|    |                     |      |                    |      |      |
| 1  |                     |      | Group 11           |      |      |
|    |                     |      |                    |      |      |
| 1  |                     |      | Group 12           |      |      |
|    |                     |      |                    |      |      |
| 1  |                     |      | Group 13           |      |      |
|    |                     |      |                    |      |      |
| 1  |                     |      | Group 14           |      |      |
|    |                     |      |                    |      |      |
| 1  |                     |      | Group 15           |      |      |
|    |                     |      |                    |      |      |
| 1  |                     |      | Group 16           |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | Esterase/lipase     | N    | At2g39420          | 93   | 2    |
|    | family protein      | P_18 |                    |      | e-18 |
|    | \[*Arabidopsis      | 1474 |                    |      |      |
|    | thaliana*\]         |      |                    |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | 60S Ribosomal       | AP00 | Translation;       | 229  | 2    |
|    | protein \[*Oryza    | 5612 | similar to L10aC   |      | e-64 |
| 1  | sativa*\]           |      |                    | 222  |      |
|    |                     | N    | Translation;       |      | 7    |
| 1  | 60S Ribosomal       | P_91 | L28-like           | 221  | e-57 |
|    | protein \[*O.       | 6542 |                    |      |      |
|    | sativa*\]           |      | Chloroplast        |      | 1    |
|    |                     | AAM6 | translation; S16   |      | e-56 |
|    | 30S ribosomal       | 3199 | (*rps16*)          |      |      |
|    | protein \[*A.       |      |                    |      |      |
|    | thaliana*\]         |      |                    |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | Phosphatase 1       | P4   | Signal             | 479  | 1e   |
|    | \[*Medicago         | 8488 | transduction; PP1; |      | -134 |
|    | sativa*\]           |      | ser/thr prot phos  |      |      |
+----+---------------------+------+--------------------+------+------+
| 2  | Amino acid          | N    | Amino acid         | 44   | 7e-4 |
|    | transporter \[*A.   | P_19 | metabolism;        |      |      |
|    | thaliana*\]         | 7770 | At5g23810          |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | Photosystem II      | BAA8 | Chloroplast        | 300  | 1e   |
|    | protein D2          | 3443 | protein associated |      | -103 |
|    | \[*Anthoceros       |      | with Photosystem   |      |      |
|    | punctata*\]         |      | II                 |      |      |
+----+---------------------+------+--------------------+------+------+
| 2  | -cyanoalanine      | AAN8 | Detoxification of  | 147  | 5    |
|    | synthetase          | 6822 | CN formed from     |      | e-35 |
|    | \[*Betula           |      | ethylene; enzyme   |      |      |
|    | pendula*\]          |      | probably located   |      |      |
|    |                     |      | to mitochondria    |      |      |
+----+---------------------+------+--------------------+------+------+
| 2  | Metallothionein     | BAA9 | Heavy metal        | 48   | 5e-5 |
|    | protein \[*Pyrus    | 6449 | homeostasis        |      |      |
|    | pyrifolia*\]        |      |                    |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | Stress-inducible    | N    | Pa                 | 86   | 2    |
|    | protein \[*O.       | P_91 | thogenesis-related |      | e-16 |
|    | sativa*\]           | 0312 | protein            |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | phi-1 \[*Nicotiana  | BAA3 | P                  | 311  | 5    |
|    | tabacum*\]          | 3810 | hosphate-inducible |      | e-84 |
|    |                     |      | gene               |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | Possible            | N    | PR protein; Lipid  | 82   | 4    |
|    | non-specific lipid  | P_91 | metabolism?        |      | e-15 |
|    | transfer protein    | 9079 |                    |      |      |
|    | \[*O. sativa*\]     |      |                    |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | Expressed Protein   | N    | At2g12905          | 57   | 5    |
|    | \[*A. thaliana*\]   | P_67 |                    |      | e-12 |
| 1  |                     | 1841 | At4g23630          | 176  |      |
|    | Expressed protein   |      |                    |      | 1    |
| 1  | \[*A. thaliana*\]   | N    | At4g31130          | 261  | e-43 |
|    |                     | P_19 |                    |      |      |
| 1  | Expressed protein   | 4094 | Similar to         | 337  | 1    |
|    | \[*A. thaliana*\]   |      | 7-transmembrane    |      | e-68 |
|    |                     | N    | and G-coupled      |      |      |
|    | Expressed protein   | P_19 | proteins           |      | 7    |
|    | \[*A. thaliana*\]   | 4842 |                    |      | e-92 |
|    |                     |      |                    |      |      |
|    |                     | N    |                    |      |      |
|    |                     | P_18 |                    |      |      |
|    |                     | 7568 |                    |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | Hypothetical        | AAP2 | At2g27280          | 171  | 4    |
|    | protein \[*O.       | 1410 |                    |      | e-42 |
| 1  | sativa*\]           |      | Related to *A.     | 61   |      |
|    |                     | CAE0 | thaliana* protein  |      | 1e-8 |
| 1  | Hypothetical        | 2140 | with heavy metal   | 221  |      |
|    | protein \[*O.       |      | domain             |      | 2    |
| 1  | sativa*\]           | A8   |                    | 109  | e-56 |
|    |                     | 4671 | At4g31130          |      |      |
| 1  | Hypothetical        |      |                    | 50   | 2    |
|    | protein \[*A.       | AAO6 |                    |      | e-31 |
| 1  | thaliana*\]         | 3778 |                    | 258  |      |
|    |                     |      |                    |      | 1e-5 |
| 1  | Hypothetical        | BAD0 |                    | 49   |      |
|    | Protein \[*Populus  | 7868 |                    |      | 7    |
|    | tremuloides*\]      |      |                    |      | e-68 |
|    |                     | AAO4 |                    |      |      |
|    | Hypothetical        | 4040 |                    |      | 2e-5 |
|    | Protein \[*O.       |      |                    |      |      |
|    | sativa*\]           | N    |                    |      |      |
|    |                     | P_91 |                    |      |      |
|    | Hypothetical        | 6003 |                    |      |      |
|    | protein \[*A.       |      |                    |      |      |
|    | thaliana*\]         |      |                    |      |      |
|    |                     |      |                    |      |      |
|    | Hypothetical        |      |                    |      |      |
|    | Protein \[*O.       |      |                    |      |      |
|    | sativa*\]           |      |                    |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | Calmodulin-binding  | N    | Calcium signaling; | 129  | 2    |
|    | protein \[*A.       | P_56 | At1g73800          |      | e-29 |
|    | thaliana*\]         | 5073 |                    |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | Wound-induced       | P2   | Defense/Stress     | 54   | 2e-6 |
|    | protein             | 0144 | related            |      |      |
|    | \[*Mesembryanthemum |      |                    |      |      |
|    | crystallinum*\]     |      |                    |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | Major allergen      | AAS4 | Defense/stress     | 156  | 1    |
|    | \[*Prunus avium*\]  | 7036 | related            |      | e-37 |
+----+---------------------+------+--------------------+------+------+
| 1  | Putative allergen   | AF13 | Defense/stress     | 196  | 1    |
|    | \[*Prunus           | 4731 | related            |      | e-47 |
|    | armeniaca*\]        |      |                    |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | Anthranilate        | N    | Amino acid         | 234  | 1    |
|    | synthase β-chain    | P_20 | metabolism (trp    |      | e-60 |
|    | \[*A. thaliana*\]   | 0597 | biosynthesis);     |      |      |
|    |                     |      | At5g57890          |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | NADH dehydrogenase, | BAC9 | Ubiquinone         | 110  | 2    |
|    | subunit 7           | 8848 | oxidoreductase;    |      | e-23 |
|    | \[*Brassica         |      | located in         |      |      |
|    | napus*\]            |      | mitochondrion;     |      |      |
|    |                     |      | Oxidative          |      |      |
|    |                     |      | phophorylation     |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | Omega-3 FA          | AAN1 | Fatty acid         | 398  | 1e   |
|    | desaturase \[*B.    | 7503 | metabolism         |      | -110 |
|    | pendula*\]          |      |                    |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  |  amylase \[*P.     | AAD3 | Starch metabolism  | 254  | 5    |
|    | armeniaca*\]        | 8148 |                    |      | e-67 |
+----+---------------------+------+--------------------+------+------+
| 1  | Keto-acyl reductase | AAB8 | Cuticle wax        | 107  | 1    |
|    | \[*Allium porrum*\] | 2764 | biosynthesis       |      | e-22 |
+----+---------------------+------+--------------------+------+------+
| 2  | 14-3-3-like protein | BAB4 | Various processes  | 359  | 5    |
|    | \[*Vigna            | 7118 | via                |      | e-98 |
|    | angularis*\]        |      | protein-protein    |      |      |
|    |                     |      | interaction        |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | Lipase/hydrolase    | N    | Has GDSL-motif;    | 291  | 7    |
|    | \[*A. thaliana*\]   | P_17 | At1g74460          |      | e-78 |
|    |                     | 7586 |                    |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | Mitochondrial ATP   | N    | G subunit;         | 115  | 4    |
|    | synthase \[*A.      | P_19 | respiration;       |      | e-25 |
|    | thaliana*\]         | 4351 | At4g26210          |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | Putative            | AAP8 | Disease            | 355  | 4    |
|    | xyloglucanase       | 4703 | resistance/defense |      | e-97 |
|    | inhibitor           |      |                    |      |      |
|    | \[*Solanum          |      |                    |      |      |
|    | tuberosum*\]        |      |                    |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | Some sort of        | AAF9 | At1g24420 and      | 134  | 8    |
|    | transferase \[*A.   | 7979 | At1g24430          |      | e-31 |
|    | thaliana*\]         |      |                    |      |      |
+----+---------------------+------+--------------------+------+------+
| 1  | S                   | AAQ1 | Intracellular      | 290  | 1    |
|    | ynptobrevin-related | 5287 | tra                |      | e-77 |
|    | protein \[*P.       |      | fficking/secretion |      |      |
|    | pyrifolia*\]        |      |                    |      |      |
+----+---------------------+------+--------------------+------+------+

Table 4. Peach Genes Up-regulated in SD at 25 °C \[BR subtraction\].

+-----+---------------------+------+--------------------+-----+------+
| No. | Gene Match          | A    | Function           | H   | E    |
| of  | Description         | cces |                    | igh | V    |
| Clo | \[Source Organism\] | sion |                    | est | alue |
| nes |                     | Nu   |                    | Sc  |      |
|     |                     | mber |                    | ore | \[   |
|     |                     |      |                    | \[  | Lowe |
|     |                     |      |                    | Bit | st\] |
|     |                     |      |                    | s\] |      |
+-----+---------------------+------+--------------------+-----+------+
| 2   | Some sort of        | N    | Most similar to    | 230 | 1    |
|     | transferase         | P_19 | UDP-g              |     | e-59 |
|     | \[*Arabidopsis      | 9780 | lycosyltransferase |     |      |
|     | thaliana*\]         |      | family; At5g49690  |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Deh                 | AAL6 | Stress related;    | 129 | 5    |
|     | ydration-responsive | 7991 | contains BURP      |     | e-29 |
|     | protein RD22        |      | domain             |     |      |
|     | \[*Gossypium        |      |                    |     |      |
|     | hirsutum*\]         |      |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | *Nif*-U-like        | AAM6 | Similar to         | 243 | 1    |
|     | protein             | 6114 | prokaryotic        |     | e-63 |
|     | (iron/sulfur        |      | N-fixing gene;     |     |      |
|     | cluster) \[*A.      |      | At4g22220          |     |      |
|     | thaliana*\]         |      |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 2   | 6-phosphoglucanate  | N    | Glycolysis or      | 407 | 1e   |
|     | dehydrogenase \[*A. | P_18 | glucose shunt      |     | -112 |
|     | thaliana*\]         | 6885 | pathway; At3g02360 |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 2   | -tubulin \[*Anemia | P3   | Microtubule        | 447 | 1e   |
|     | phyllitidis*\]      | 3623 | formation          |     | -125 |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Mic                 | BAD0 | Light chain 3;     | 202 | 2    |
|     | rotubule-associated | 5590 | aids in            |     | e-51 |
|     | protein \[*Oryza    |      | microtubule        |     |      |
|     | sativa*\]           |      | assembly           |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | hydroxyproline-rich | AAL3 | Possible cell wall | 200 | 4    |
|     | glycoprotein        | 1182 | protein; At4g14900 |     | e-51 |
|     | homolog \[*A.       |      |                    |     |      |
|     | thaliana*\]         |      |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | 40S ribosomal       | N    | Translation;       | 325 | 4    |
|     | protein \[*A.       | P_19 | S6-like (*rps6B*)  |     | e-88 |
| 1   | thaliana*\]         | 6598 | At5g10360          | 92  |      |
|     |                     |      |                    |     | 3    |
| 2   | 40S ribosomal       | N    | Translation;       | 192 | e-18 |
|     | protein \[*A.       | P_19 | S20-like (*rps20B* |     |      |
|     | thaliana*\]         | 0321 | & *C*); At3g47370  |     | 1    |
|     |                     |      |                    |     | e-48 |
|     | 60S ribosomal       | AAK2 | L17; cytoplasmic   |     |      |
|     | protein \[*Castanea | 5758 | translation;       |     |      |
|     | sativa*\]           |      | wound-inducible    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Heat shock protein  | P3   | Stress related;    | 459 | 1e   |
|     | 82 \[*Nicotiana     | 6182 | hsp 90 family      |     | -128 |
|     | tabacum*\]          |      |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Heat shock protein  | AAD1 | DnaJ protein       | 275 | 4    |
|     | \[*Hevea            | 2055 |                    |     | e-73 |
|     | brasiliensis*\]     |      |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | LMW Heat Shock      | AF15 | Class II; match in | 410 | 1e   |
|     | protein \[*Prunus   | 9562 | BLASTn             |     | -112 |
|     | dulcis*\]           |      |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 2   | Class I chitinase   | N    | Defense/Stress     | 192 | 2    |
|     | \[*A. thaliana*\]   | P_18 | response;          |     | e-48 |
|     |                     | 8317 | At3g16920          |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Ub                  | AAF7 | Targeted protein   | 289 | 1    |
|     | iquitin-conjugating | 3016 | degradation        |     | e-77 |
|     | protein, E2         |      | pathway            |     |      |
|     | \[*Avicennia        |      |                    |     |      |
|     | marina*\]           |      |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | rRNA intron homing  | AAK1 | Group I introns;   | 122 | 1    |
|     | endonuclease \[*O.  | 3589 | usually organellar |     | e-26 |
|     | sativa*\]           |      |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Pectinesterase      | N    | Cell wall          | 327 | 8    |
|     | \[*A. thaliana*\]   | P_56 | metabolism;        |     | e-97 |
|     |                     | 9041 | At5g66920          |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 2   | Zinc finger protein | N    | Transcription      | 282 | 4    |
|     | \[*A. thaliana*\]   | P_19 | factor;            |     | e-75 |
|     |                     | 1307 | PMZ-related;       |     |      |
|     |                     |      | At3g57480          |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Homeodomain protein | AAM9 | Transcriptional    | 387 | e    |
|     | \[*Gossypium        | 7321 | control; protein   |     | -119 |
|     | hirsutum*\]         |      | GhHOX1             |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Nucleic acid        | AAM6 | Transcription or   | 247 | 2    |
|     | binding protein     | 7293 | translation; has   |     | e-64 |
|     | \[*A. thaliana*\]   |      | RNA recognition    |     |      |
|     |                     |      | motifs; At3g19130  |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Expressed protein   | N    | Similarity to      | 174 | 1    |
|     | \[*A. thaliana*\]   | P_19 | reticulon protein  |     | e-42 |
| 3   |                     | 4094 | family; At4g23630  | 69  |      |
|     | Hypothetical        |      |                    |     | 2    |
|     | protein \[*O.       | N    |                    |     | e-11 |
|     | sativa*\]           | P_91 |                    |     |      |
|     |                     | 0689 |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+

+-----+---------------------+------+--------------------+-----+------+
| 2   | Ade                 | AAO7 |                    | 431 | 1e   |
|     | nosylhomocysteinase | 2664 |                    |     | -120 |
|     | \[*O. sativa*\]     |      |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 2   | Expressed protein   | N    | At5g53880          | 55  | 3    |
|     | \[*A. thaliana*\]   | P_56 |                    |     | e-07 |
|     |                     | 8802 |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | NAD-dependent       | AAL1 | Re-fixation of     | 419 | 1e   |
|     | malate              | 1502 | CO~2~ and fruit    |     | -116 |
|     | dehydrogenase       |      | acidity            |     |      |
|     | \[*Prunus           |      |                    |     |      |
|     | persica*\]          |      |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Cytochrome b6-f     | P1   | Subunit VIII;      | 59  | 2    |
|     | complex             | 2177 | oxidative          |     | e-08 |
|     | \[*Marchantia       |      | phosphorylation    |     |      |
|     | polymorpha*\]       |      |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 2   | Chalcone synthase   | BAB9 | Anthocyanin        | 309 | 2    |
|     | \[*Malus* X         | 2996 | biosynthesis;      |     | e-83 |
|     | *domestica*\]       |      | defense            |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Chloroplast         | AY36 | Match is to the 5' | 274 | 1    |
|     | maturase \[*Rubus   | 6358 | UTR in BLASTn      |     | e-70 |
|     | chamaemorus*\]      |      |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Similar to myb      | AAK1 | Transcriptional    | 100 | 1    |
|     | proteins \[*G.      | 9611 | control            |     | e-20 |
|     | hirsutum*\]         |      |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Putative extensin   | CAA3 | \[sequence very    | 31  | 8.3  |
|     | \[*Lycopersicon     | 9217 | short, but match   |     |      |
|     | esculentum*\]       |      | is good despite    |     |      |
|     |                     |      | high e value\]     |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Unknown             |      | Group 17           |     |      |
|     |                     |      |                    |     |      |
| 1   |                     |      | Group 18           |     |      |
|     |                     |      |                    |     |      |
| 2   |                     |      | Group 19           |     |      |
|     |                     |      |                    |     |      |
| 1   |                     |      | Group 20           |     |      |
|     |                     |      |                    |     |      |
| 1   |                     |      | Group 21           |     |      |
|     |                     |      |                    |     |      |
| 1   |                     |      | Group 22           |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | RAD23-like \[*L.    | CAB5 | Association with   | 57  | 2    |
|     | esculentum*\]       | 1544 | ubiquitinated      |     | e-07 |
|     |                     |      | proteins           |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Abnormal            | N    | Multifunctional    | 125 | 3    |
|     | inflorescence       | P_19 | fatty-acid         |     | e-43 |
|     | meristem \[*A.      | 4630 | metabolism         |     |      |
|     | thaliana*\]         |      | protein; At4g29010 |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | SAM synthetase      | Q9   | SAM synthase 2     | 164 | 5    |
|     | \[*Caranthus        | 6552 |                    |     | e-40 |
|     | roseus*\]           |      |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Casein kinase \[*O. | N    | Signal             | 193 | 8    |
|     | sativa*\]           | P_91 | transduction       |     | e-49 |
|     |                     | 6323 |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Mitochondrial       | N    | Mitochondrial      | 254 | 2    |
|     | carrier protein     | P_56 | transport;         |     | e-66 |
|     | \[*A. thaliana*\]   | 8317 | At5g15640          |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Major latex protein | CAA0 | Defense            | 89  | 3    |
|     | \[*Fragaria         | 4770 |                    |     | e-17 |
|     | vesca*\]            |      |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+
| 1   | Glycera             | CAC8 | Glycolysis         | 348 | 7    |
|     | ldehyde-3-phosphate | 0375 |                    |     | e-95 |
|     | dehydrogenase       |      |                    |     |      |
|     | \[*Capsicum         |      |                    |     |      |
|     | annuum*\]           |      |                    |     |      |
+-----+---------------------+------+--------------------+-----+------+

Table 5. Peach Genes Down-regulated in SD at 5 °C \[CF subtraction\].

+-----+---------------------+------+---------------------+------+-----+
| No. | Gene Match          | A    | Function            | Hig  | E   |
| of  | Description         | cces |                     | hest | Va  |
| Clo | \[Source organism\] | sion |                     | S    | lue |
| nes |                     | Nu   |                     | core |     |
|     |                     | mber |                     | \[Bi | \   |
|     |                     |      |                     | ts\] | [Lo |
|     |                     |      |                     |      | wes |
|     |                     |      |                     |      | t\] |
+-----+---------------------+------+---------------------+------+-----+
| 2   | Unknown             |      | Group 1             |      |     |
|     |                     |      |                     |      |     |
| 1   |                     |      | Group 23            |      |     |
|     |                     |      |                     |      |     |
| 1   |                     |      | Group 24            |      |     |
|     |                     |      |                     |      |     |
| 1   |                     |      | Group 4             |      |     |
+-----+---------------------+------+---------------------+------+-----+
| 1   | Probable            | N    | Contains a          | 130  | 2e  |
|     | steroid-binding     | P_19 | heme/cytb5 domain   |      | -29 |
|     | protein \[*Oryza    | 0458 |                     |      |     |
|     | sativa*\]           |      |                     |      |     |
+-----+---------------------+------+---------------------+------+-----+
| 1   | M                   | AAF7 | Differes slightly   | 74   | 1e  |
|     | etallothionein-like | 8509 | from CR30           |      | -12 |
|     | protein \[*Pyrus    |      |                     |      |     |
|     | pyrifolia*\]        |      |                     |      |     |
+-----+---------------------+------+---------------------+------+-----+
| 1   | AMP-binding protein | BAA9 | AM                  | 243  | 6e  |
|     | \[*Arabidopsis      | 4975 | P-synthetase/ligase |      | -64 |
|     | thaliana*\]         |      | family protein;     |      |     |
|     |                     |      | located on          |      |     |
|     |                     |      | chromosome 3        |      |     |
+-----+---------------------+------+---------------------+------+-----+
| 1   | SKP1-like protein   | CAE0 | F-box domain        | 85   | 5e  |
|     | \[*O. sativa*\]     | 3998 | protein family      |      | -16 |
+-----+---------------------+------+---------------------+------+-----+
| 1   | Expressed protein   | N    | Similar to          | 79   | 1e  |
|     | \[*A. thaliana*\]   | P_56 | p                   |      | -14 |
|     |                     | 6400 | hosphatidylglycerol |      |     |
|     |                     |      | and                 |      |     |
|     |                     |      | p                   |      |     |
|     |                     |      | hosphatidylinositol |      |     |
|     |                     |      | transfer proteins;  |      |     |
|     |                     |      | contains ML domain; |      |     |
|     |                     |      | At3g11780           |      |     |
+-----+---------------------+------+---------------------+------+-----+
| 1   | AUX/IAA Family      | N    | Responds to auxin;  | 54   | 8   |
|     | \[*A. thaliana*\]   | P_19 | may have            |      | e-7 |
|     |                     | 4637 | transcription       |      |     |
|     |                     |      | factor activity;    |      |     |
|     |                     |      | At4g29080           |      |     |
+-----+---------------------+------+---------------------+------+-----+
| 1   | 50S ribosomal       | N    | Chloroplast         | 243  | 2e  |
|     | protein \[*Spinacia | P_05 | translation; L16    |      | -63 |
| 1   | oleraceae*\]        | 4972 |                     | 111  |     |
|     |                     |      | Translation; RPS4A  |      | 2e  |
| 2   | 40S ribosomal       | N    | & D; contains an    | 120  | -23 |
|     | protein \[*O.       | P_91 | RNA binding site    |      |     |
|     | sativa*\]           | 8883 | also found in some  |      | 1e  |
|     |                     |      | stress proteins     |      | -26 |
|     | 60S ribosomal       | AAK2 |                     |      |     |
|     | protein \[*Castanea | 5760 | Translation;        |      |     |
|     | sativa*\]           |      | L35aA-D;            |      |     |
|     |                     |      | wound-inducible     |      |     |
+-----+---------------------+------+---------------------+------+-----+
| 1   | C2                  | N    | C2 domain is        | 307  | 2e  |
|     | domain-containing   | P_20 | involved in         |      | -82 |
|     | protein \[*A.       | 0364 | Ca2^+^-dependent    |      |     |
|     | thaliana*\]         |      | membrane-targeting  |      |     |
|     |                     |      | associated with     |      |     |
|     |                     |      | signal transduction |      |     |
|     |                     |      | and membrane        |      |     |
|     |                     |      | trafficking;        |      |     |
|     |                     |      | At5g55530           |      |     |
+-----+---------------------+------+---------------------+------+-----+
| 1   | Auxin efflux        | N    | Auxin transport;    | 114  | 7e  |
|     | carrier protein     | P_56 | At1g76520           |      | -25 |
|     | family \[*A.        | 5133 |                     |      |     |
|     | thaliana*\]         |      |                     |      |     |
+-----+---------------------+------+---------------------+------+-----+
| 1   | Putative            | AAL6 | Stress response;    | 100  | 6e  |
|     | dessi               | 6195 | LEA homologue       |      | -21 |
|     | cation-protectorant |      |                     |      |     |
|     | protein \[*Pyrus    |      |                     |      |     |
|     | communis*\]         |      |                     |      |     |
+-----+---------------------+------+---------------------+------+-----+
| 1   | Putative            | BAC4 | Also similar to     | 225  | 6e  |
|     | chloroplastic       | 3491 | salt-inducible      |      | -58 |
|     | RNA-binding protein |      | protein from *A.    |      |     |
|     | \[*A. thaliana*\]   |      | thaliana*;          |      |     |
|     |                     |      | At4g16390           |      |     |
+-----+---------------------+------+---------------------+------+-----+
| 1   | Mitochondrial ATP   | P2   | Respiration         | 327  | 2e  |
|     | synthase, beta      | 9685 |                     |      | -88 |
|     | chain \[*Hevea      |      |                     |      |     |
|     | brasiliensis*\]     |      |                     |      |     |
+-----+---------------------+------+---------------------+------+-----+
| 1   | Se                  | N    | Ccontains a         | 100  | 1e  |
|     | nescence-associated | P_17 | transmembrane 4     |      | -23 |
|     | protein \[*A.       | 9548 | family signature;   |      |     |
|     | thaliana*\]         |      | At2g19580           |      |     |
+-----+---------------------+------+---------------------+------+-----+
| 1   | 14-3-3-like protein | AAF2 | Different allele    | 167  | 1e  |
|     | \[*Euphorbia        | 7931 | from CR90A-02; may  |      | -41 |
|     | esula*\]            |      | associate with G    |      |     |
|     |                     |      | box DNA-binding     |      |     |
|     |                     |      | complex             |      |     |
+-----+---------------------+------+---------------------+------+-----+
| 1   | Protease-related    | N    | Contains ThiJ/PfpI  | 133  | 1e  |
|     | \[*A. thaliana*\]   | P_18 | family signature;   |      | -30 |
|     |                     | 6921 | At3g02720           |      |     |
+-----+---------------------+------+---------------------+------+-----+
| 1   | AP2-domain          | AAC2 | Probably a          | 92   | 3e  |
|     | containing protein  | 4587 | transcription       |      | -18 |
|     | \[*Prunus           |      | factor              |      |     |
|     | armeniaca\]*        |      |                     |      |     |
+-----+---------------------+------+---------------------+------+-----+

Table 6. Peach Genes Up-regulated in SD at 5 °C \[CR subtraction\].

+-----+---------------------+------+----------------------+------+----+
| No. | Gene Match          | A    | Function             | Hig  | E  |
| of  | Description         | cces |                      | hest | V  |
| Clo | \[Source organism\] | sion |                      | S    | al |
| nes |                     | Nu   |                      | core | ue |
|     |                     | mber |                      | \[Bi | \[ |
|     |                     |      |                      | ts\] | Lo |
|     |                     |      |                      |      | we |
|     |                     |      |                      |      | st |
|     |                     |      |                      |      | \] |
+-----+---------------------+------+----------------------+------+----+
| 1   | PDR-like ABC        | CAD5 | ATP-binding cassette | 105  | 5  |
|     | transporter         | 9574 | (ABC) transporters   |      | e- |
|     | \[*Oryza sative*\]  |      | control efflux and   |      | 33 |
|     |                     |      | influx of a variety  |      |    |
|     |                     |      | of substances across |      |    |
|     |                     |      | cellular membranes.  |      |    |
+-----+---------------------+------+----------------------+------+----+
| 1   | Oxidoreductase      | N    | Similar to           | 298  | 7  |
|     | family              | P_17 | *Eucalyptus*         |      | e- |
|     | \[*Arabidopsis      | 7021 | cinnamoyl CoA        |      | 80 |
|     | thaliana*\]         |      | reductase; At1g68540 |      |    |
+-----+---------------------+------+----------------------+------+----+
| 1   | Similar to blue     | BAB0 | Electron transfer?   | 57   | 6  |
|     | copper protein      | 2059 |                      |      | e- |
|     | \[*A. thaliana*\]   |      |                      |      | 08 |
+-----+---------------------+------+----------------------+------+----+
| 1   | Expressed protein   | N    | At2g36485            | 105  | 4  |
|     | \[*A. thaliana*\]   | P_56 |                      |      | e- |
|     |                     | 5849 |                      |      | 22 |
+-----+---------------------+------+----------------------+------+----+
| 3   | Class II chitinase  | AAM1 | Defense/stress       | 285  | 2  |
|     | \[*Malus x          | 2890 | response             |      | e- |
|     | domestica*\]        |      |                      |      | 76 |
+-----+---------------------+------+----------------------+------+----+
| 1   | SAM decarboxylase   | BAC5 | Decarboxylated SAM   | 346  | 1  |
|     | \[*Malus x          | 5114 | is a substrate for   |      | e- |
|     | domestica*\]        |      | synthesis of         |      | 94 |
|     |                     |      | spermidine and       |      |    |
|     |                     |      | spermine             |      |    |
+-----+---------------------+------+----------------------+------+----+
| 1   | 60S ribosomal       | N    | Translation; subunit | 126  | 1  |
|     | protein \[*A.       | P_17 | L34A; At1g26880      |      | e- |
| 2   | thaliana*\]         | 4010 |                      | 284  | 28 |
|     |                     |      | Translation; subunit |      |    |
| 1   | 60S ribosomal       | N    | L10aB; At2g27530     | 157  | 7  |
|     | protein \[*A.       | P_56 |                      |      | e- |
| 1   | thaniana*\]         | 5654 | Translation; subunit | 199  | 76 |
|     |                     |      | L10 = RPL10B         |      |    |
|     | 60S ribosomal       | Q4   |                      |      | 3  |
|     | protein \[*N.       | 0592 | Translation; subunit |      | e- |
|     | tabacum*\]          |      | L21 = RPL21A-F \[*A. |      | 38 |
|     |                     | T5   | thaliana*\]          |      |    |
|     | 60S ribosomal       | 0602 |                      |      | 1  |
|     | protein \[*O.       |      |                      |      | e- |
|     | sativa*\]           |      |                      |      | 50 |
+-----+---------------------+------+----------------------+------+----+
| 1   | M                   | U9   | Seems to be somewhat | 87   | 2  |
|     | etallothionein-like | 7494 | different from       |      | e- |
|     | protein \[*Prunus   |      | CF78A-01             |      | 16 |
|     | armeniaca*\]        |      |                      |      |    |
+-----+---------------------+------+----------------------+------+----+
| 1   | Mitochondrial       | AAM4 | ε subunit; At1g51650 | 99   | 4  |
|     | F1-ATPase \[*A.     | 7859 |                      |      | e- |
|     | thaliana*\]         |      |                      |      | 20 |
+-----+---------------------+------+----------------------+------+----+
| 1   | -1,3- glucanase    | BAC6 | Defense/stress       | 337  | 1  |
|     | \[*Fragaria* *x*    | 6141 | response             |      | e- |
|     | *ananassa*\]\]      |      |                      |      | 91 |
+-----+---------------------+------+----------------------+------+----+
| 5   | Unknown             |      | Group 1              |      |    |
|     |                     |      |                      |      |    |
| 2   |                     |      | Group 3              |      |    |
|     |                     |      |                      |      |    |
| 2   |                     |      | Group 25             |      |    |
|     |                     |      |                      |      |    |
| 1   |                     |      | Group 26             |      |    |
+-----+---------------------+------+----------------------+------+----+
| 1   | Hypothetical        | N    |                      | 69   | 2  |
|     | protein \[*O.       | P_91 |                      |      | e- |
|     | sativa*\]           | 0689 |                      |      | 11 |
+-----+---------------------+------+----------------------+------+----+
| 1   | Acetyl              | AAL1 | Has a thiolase       | 152  | 3  |
|     | CoA-ace             | 8928 | domain; may be       |      | e- |
|     | tyltransferase-like |      | associated with      |      | 36 |
|     | \[*H*.              |      | fatty acid oxidation |      |    |
|     | *brasiliensis*\]    |      | or steroid           |      |    |
|     |                     |      | biosynthesis         |      |    |
+-----+---------------------+------+----------------------+------+----+
| 1   | Methionine synthase | AAF2 | Met metabolism       | 296  | 1  |
|     | \[*Coffea           | 6735 |                      |      | e- |
|     | arabica*\]          |      |                      |      | 79 |
+-----+---------------------+------+----------------------+------+----+
| 1   | PRU major allergen  | AAS4 | Defense/stress       | 134  | 6  |
|     | \[*Prunus avium*\]  | 7035 | response             |      | e- |
|     |                     |      |                      |      | 31 |
+-----+---------------------+------+----------------------+------+----+
| 1   | Chitinase I         | Q9   | Defense/stress       | 275  | 3  |
|     | \[*Tulipa bakeri*\] | SLP4 | response             |      | e- |
|     |                     |      |                      |      | 77 |
+-----+---------------------+------+----------------------+------+----+
| 1   | 14-3-3-like Protein | AAC1 | Involved in a        | 362  | 4  |
|     | \[*Maackia          | 5418 | variety of different |      | e- |
|     | amurensis*\]        |      | cellular processes;  |      | 99 |
|     |                     |      | binds other proteins |      |    |
+-----+---------------------+------+----------------------+------+----+

Table 7. Peach Genes Up-regulated at 5 °C in SD \[EF subtraction\].

+-----+---------------------+------+----------------------+------+----+
| No. | Gene Match          | A    | Function             | Hig  | E  |
| of  | Description         | cces |                      | hest | V  |
| Clo | \[Source organism\] | sion |                      | S    | al |
| nes |                     | Nu   |                      | core | ue |
|     |                     | mber |                      | \[Bi | \[ |
|     |                     |      |                      | ts\] | Lo |
|     |                     |      |                      |      | we |
|     |                     |      |                      |      | st |
|     |                     |      |                      |      | \] |
+-----+---------------------+------+----------------------+------+----+
| 3   | Thaumatin \[*Prunus | P8   | Defense; PR gene;    | 273  | 2  |
|     | persica*\]          | 3335 | *PpAZ8*              |      | e- |
|     |                     |      |                      |      | 72 |
+-----+---------------------+------+----------------------+------+----+
| 2   | ClassIV chitinase   | CAA7 | Defense/stress       | 181  | 6  |
|     | \[*A. thaliana*\]   | 4930 | response; At3g54420  |      | e- |
|     |                     |      |                      |      | 45 |
+-----+---------------------+------+----------------------+------+----+
| 1   | 40S ribosomal       | P1   | Cytosolic ribosomal  | 117  | 6  |
|     | protein \[*Glycine  | 7093 | protein, S11 =       |      | e- |
|     | max*\]              |      | RPSA-C \[*A.         |      | 26 |
|     |                     |      | thaliana*\]          |      |    |
+-----+---------------------+------+----------------------+------+----+
| 1   | Possible            | X9   | May have nucleotide  | 64   | 2e |
|     | transcription       | 7907 | binding properties   |      | -7 |
|     | factor \[*Vicia     |      | \[match in BLASTn\]  |      |    |
|     | faba*\]             |      |                      |      |    |
+-----+---------------------+------+----------------------+------+----+
| 1   | P                   | P8   | Defense/stress       | 213  | 7  |
|     | athogenesis-related | 3343 | response; *PpAz89*   |      | e- |
|     | protein PR-4 \[*P.  |      |                      |      | 55 |
|     | persica*\]          |      |                      |      |    |
+-----+---------------------+------+----------------------+------+----+
| 2   | Lea-like protein    | P3   | Similar to ARG2      | 86   | 3  |
|     | \[*Vigna radiata*\] | 2292 | which is             |      | e- |
|     |                     |      | IAA-induced. Also    |      | 16 |
|     |                     |      | induced by heat,     |      |    |
|     |                     |      | ethylene, wounding,  |      |    |
|     |                     |      | tuberization         |      |    |
+-----+---------------------+------+----------------------+------+----+
| 1   | Similar to Tar1p    | N    | Similar to cotton    | 49   | 9e |
|     | \[*Saccharomyces    | P_69 | and rose ESTs and a  |      | -6 |
|     | cerevesiae*\]       | 0845 | rice genomic clone   |      |    |
|     |                     |      | \[BLASTn score =     |      |    |
|     |                     |      | 462, E = 1e-137\]    |      |    |
+-----+---------------------+------+----------------------+------+----+
| 1   | Expressed protein   | AJ82 | EST from             | 333  | 1  |
|     | \[*P. persica*\]    | 6928 | preclimacteric to    |      | e- |
|     |                     |      | climacteric fruit    |      | 88 |
|     |                     |      | mesocarp             |      |    |
+-----+---------------------+------+----------------------+------+----+
| 1   | Phase-change        | AJ27 | Developmental stage  | 56   | 7e |
|     | protein \[*Quercus  | 1778 | regulated;           |      | -5 |
|     | robur*\]            |      | \[BLASTn\]           |      |    |
+-----+---------------------+------+----------------------+------+----+
| 1   | Pollen coat-like    | AAM6 | Note: also somewhat  | 89   | 2  |
|     | protein \[*A.       | 5256 | similar to kin1      |      | e- |
|     | thaliana*\]         |      | At5g38760            |      | 17 |
+-----+---------------------+------+----------------------+------+----+
| 1   | M                   | BAA9 | Heavy metal          | 55   | 6e |
|     | etallothionein-like | 6449 | homeostasis          |      | -7 |
|     | protein (*Pyrus     |      |                      |      |    |
|     | pyrifolia*)         |      |                      |      |    |
+-----+---------------------+------+----------------------+------+----+
| 1   | Dehydrin \[*P.      | AAC4 | Stress responses;    | 101  | 4  |
|     | persica*\]          | 9658 | *Ppdhn1*             |      | e- |
|     |                     |      |                      |      | 21 |
|     |                     | CAC0 |                      |      |    |
|     |                     | 0637 |                      |      |    |
+-----+---------------------+------+----------------------+------+----+
| 1   | Possible WD-40      | N    | Could be a           | 199  | 3  |
|     | repeat protein      | P_18 | transducin;          |      | e- |
|     | \[*A. thaliana*\]   | 1567 | At2g40360            |      | 50 |
+-----+---------------------+------+----------------------+------+----+
| 1   | Unknown             |      | Group 27             |      |    |
|     |                     |      |                      |      |    |
| 1   |                     |      | Group 1              |      |    |
|     |                     |      |                      |      |    |
| 1   |                     |      | Group 28             |      |    |
+-----+---------------------+------+----------------------+------+----+

Table 8. Peach Genes Down-regulated at 5 °C in SD \[ER subtraction\].

+------+----------------------+-------+-------------------+------+----+
| No.  | Gene Match           | Acce  | Function          | Hig  | E  |
| of   | Description \[Source | ssion |                   | hest | V  |
| Cl   | organism\]           | N     |                   | S    | al |
| ones |                      | umber |                   | core | ue |
|      |                      |       |                   | \[Bi | \[ |
|      |                      |       |                   | ts\] | Lo |
|      |                      |       |                   |      | we |
|      |                      |       |                   |      | st |
|      |                      |       |                   |      | \] |
+------+----------------------+-------+-------------------+------+----+
| > 2  | ADP-ribosylation     | AAP   | Vesicular         | 310  | 8  |
| >    | factor \[*Oryza      | 73857 | trafficking       |      | e- |
| > 1  | sativa*\]            |       |                   | 308  | 84 |
|      |                      | O     |                   |      |    |
|      | Same \[*Vigna        | 48920 |                   |      | 3  |
|      | unguiculata*\]       |       |                   |      | e- |
|      |                      |       |                   |      | 83 |
+------+----------------------+-------+-------------------+------+----+
| > 1  | Major latex protein  | CAA   | Ripening-induced  | 92   | 3  |
|      | \[*Fragaria vesca*\] | 04770 |                   |      | e- |
|      |                      |       |                   |      | 18 |
+------+----------------------+-------+-------------------+------+----+
| > 1  | Hypothetical protein | AAM   | Has ZIM motif     | 65   | 8  |
| >    | \[*Arabidopsis       | 65383 | related to DNA    |      | e- |
| > 1  | thaliana*\]          |       | binding           | 112  | 23 |
| >    |                      | T     |                   |      |    |
| > 2  | Hypothetical protein | 51098 | AN1-like Zn       | 90   | 2  |
| >    | \[*Prunus            |       | finger            |      | e- |
| > 1  | armeniaca*\]         | NP_1  |                   | 97   | 24 |
| >    |                      | 73656 | Could be a        |      |    |
| > 1  | Hypothetical protein |       | glu               | 71   | 1  |
| >    | \[*A. thaliana*\]    | CAB   | cosyltransferase; |      | e- |
| > 1  |                      | 79859 | At1g22400         | 70   | 17 |
|      | Hypothetical         |       |                   |      |    |
|      | proteins \[*A.       | BAB   | At4g31410         |      | 2  |
|      | thaliana*\]          | 33421 |                   |      | e- |
|      |                      |       | Chloroplast       |      | 19 |
|      | Putative             | T     | protein           |      |    |
|      | s                    | 08999 |                   |      | 9  |
|      | enescence-associated |       |                   |      | e- |
|      | protein \[*Pisum     |       |                   |      | 12 |
|      | sativum*\]           |       |                   |      |    |
|      |                      |       |                   |      | 2  |
|      | Hypothetical protein |       |                   |      | e- |
|      | \[*Spinacia          |       |                   |      | 11 |
|      | oleraces*\]          |       |                   |      |    |
+------+----------------------+-------+-------------------+------+----+
| > 2  | Tubulin alpha-1      | AAK   | Microtubule       | 361  | 8  |
|      | chain \[*Rosa        | 81858 | assembly          |      | e- |
|      | hybrida*\]           |       |                   |      | 99 |
+------+----------------------+-------+-------------------+------+----+
| > 1  | Unknown              |       | Group 29          |      |    |
| >    |                      |       |                   |      |    |
| > 1  |                      |       | Group 30          |      |    |
| >    |                      |       |                   |      |    |
| > 1  |                      |       | Group 31          |      |    |
| >    |                      |       |                   |      |    |
| > 1  |                      |       | Group 32          |      |    |
| >    |                      |       |                   |      |    |
| > 1  |                      |       | Group 33          |      |    |
| >    |                      |       |                   |      |    |
| > 1  |                      |       | Group 34          |      |    |
| >    |                      |       |                   |      |    |
| > 2  |                      |       | Group 35          |      |    |
| >    |                      |       |                   |      |    |
| > 1  |                      |       | Group 36          |      |    |
+------+----------------------+-------+-------------------+------+----+
| > 2  | DNA binding protein  | NP_5  | Similar to        | 150  | 3  |
|      | \[*A. thaliana*\]    | 68755 | EREBP-4;          |      | e- |
|      |                      |       | At5g51190         |      | 35 |
+------+----------------------+-------+-------------------+------+----+
| > 1  | Ubiquitin-specific   | AAM   | Targeted protein  | 207  | 2  |
|      | protease 14 \[*A.    | 98237 | turnover; various |      | e- |
|      | thaliana*\]          |       | processes;        |      | 52 |
|      |                      |       | At3g206625 and    |      |    |
|      |                      |       | At3g206230        |      |    |
+------+----------------------+-------+-------------------+------+----+
| > 1  | caffeoyl-CoA         | AAB   | Lignin            | 322  | 2  |
|      | 3                    | 80931 | biosynthesis      |      | e- |
|      | -O-methyltransferase |       |                   |      | 87 |
|      | 5 \[*Nicotiana       |       |                   |      |    |
|      | tabacum*\]           |       |                   |      |    |
+------+----------------------+-------+-------------------+------+----+
| > 1  | Expressed protein    | NP_5  | Pfam profile      | 205  | 3  |
| >    | \[*A. thaliana*\]    | 66687 | PF05078: dom:     |      | e- |
| > 1  |                      |       | DUF679; At3g21550 | 97   | 52 |
|      | Expressed protein    | NP_5  |                   |      |    |
|      | \[*A. thaliana*\]    | 67874 | At4g31410         |      | 2  |
|      |                      |       |                   |      | e- |
|      |                      |       |                   |      | 19 |
+------+----------------------+-------+-------------------+------+----+
| > 1  | Actin \[*G.          | AAP   | Cytoskeleton      | 270  | 9  |
|      | hirsutum*\]          | 73457 |                   |      | e- |
|      |                      |       |                   |      | 72 |
+------+----------------------+-------+-------------------+------+----+
| > 1  | Actin depolymerizing | Q     | Cytoskeleton      | 187  | 2  |
|      | factor 2 \[*Petunia  | 9FVI1 |                   |      | e- |
|      | hybrida*\]           |       |                   |      | 46 |
+------+----------------------+-------+-------------------+------+----+
| > 1  | homeodomain-leucine  | AAF   | does not overlap  | 94   | 6  |
|      | zipper protein 56    | 01764 | homeobox domain   |      | e- |
|      | \[*Glycine max*\]    |       |                   |      | 18 |
+------+----------------------+-------+-------------------+------+----+
| > 2  | Pectinacetylesterase | NP_9  | At5g23870         | 281  | 5  |
|      | \[*A. thaliana*\]    | 74826 |                   |      | e- |
|      |                      |       |                   |      | 75 |
+------+----------------------+-------+-------------------+------+----+
| > 1  | Putative RING-H2     | BAC   | Similar to RHF2a; | 68   | 9  |
|      | finger protein \[*A. | 42950 | component of E3   |      | e- |
|      | thaliana*\]          |       | ligase \[SCF      |      | 11 |
|      |                      |       | complex\];        |      |    |
|      |                      |       | At5g22000         |      |    |
+------+----------------------+-------+-------------------+------+----+
| > 3  | Gibberellin-induced  | P     | Root-associated   | 162  | 8  |
|      | protein              | 47926 |                   |      | e- |
|      | \[*Lycopersicon      |       |                   |      | 39 |
|      | esculentum*\]        |       |                   |      |    |
+------+----------------------+-------+-------------------+------+----+
| > 1  | *Phi-1*-like \[*A.   | NP_1  | P                 | 138  | 3  |
| >    | thaliana*\]          | 99968 | hosphate-induced; |      | e- |
| > 1  |                      |       | Pfam profile      | 419  | 32 |
|      | *Phi-1* \[*N.        | BAA   | PF04674;          |      |    |
|      | tabacum*\]           | 33810 | At5g51550         |      | 1e |
|      |                      |       |                   |      | -1 |
|      |                      |       |                   |      | 16 |
+------+----------------------+-------+-------------------+------+----+
| > 1  | Upstream binding     | NP_0  | Possible          | 34   | 1  |
|      | factor \[*Mus        | 38727 | transcription     |      | .1 |
|      | musculus*\]          |       | factor; match is  |      |    |
|      |                      |       | not very good     |      |    |
+------+----------------------+-------+-------------------+------+----+
| > 1  | Phloem-specific      | S     | Preferentially    | 50   | 1e |
|      | protein \[*Vicia     | 66340 | expressed in      |      | -5 |
|      | faba*\]              |       | aerial plant      |      |    |
|      |                      |       | organs            |      |    |
+------+----------------------+-------+-------------------+------+----+
| > 1  | Mann                 | AAF   |                   | 32   | 5  |
|      | osyl-oligosaccharide | 16414 |                   |      | .3 |
|      | 1,2-α -mannosidase   |       |                   |      |    |
|      | \[*G. max*\]         |       |                   |      |    |
+------+----------------------+-------+-------------------+------+----+
| > 1  | putative permease 1  | AAK   | Integral membrane | 183  | 8  |
|      | \[*A. thaliana*\]    | 59508 | proteins involved |      | e- |
|      |                      |       | in the transport  |      | 46 |
|      |                      |       | of substrates     |      |    |
|      |                      |       | into the cell;    |      |    |
|      |                      |       | At5g62890         |      |    |
+------+----------------------+-------+-------------------+------+----+
| > 1  | Translationally      | P     | Has high homology | 110  | 1  |
|      | controlled tumor     | 35681 | to human and      |      | e- |
|      | protein homolog      |       | yeast;            |      | 23 |
|      | (TCTP) \[*O.         |       | housekeeping      |      |    |
|      | sativa*\]            |       | function?         |      |    |
+------+----------------------+-------+-------------------+------+----+
| > 1  | Dehydration-induced  | NP_5  | ERD3-like; may    | 216  | 7  |
|      | protein \[*A*.       | 67427 | have ankyrin      |      | e- |
|      | *thaliana*\]         |       | repeats;          |      | 56 |
|      |                      |       | At4g14360         |      |    |
+------+----------------------+-------+-------------------+------+----+