Enzyme / Code / EC / Conserved
sequences / Expected
Length (bp) / ID of example protein
Acid -galactosidase / AAG / 3.2.1.22 / F – NI/LDDCW
R –WNDPDM
F2 –ASWGID
R2 - EVWAGP / 510
522 / CAC08337 (A.t.)
Neutral
-galactosidase / NAG / 3.2.1.22 / F – WWMTQR
R – WCTWDA
F5' MTVGAG
R2 - IDDGWA / 400
730 / AAF79504 (A.t.)
Acid invertase / AIN / 3.2.1.26 / F – VPPPGIG/D
R - VDHSIVE / 1030 / AAA34132 (L.e.)
Neutral invertase / NIN / 3.2.1.26 / F – DGFDMFP
R - PKNTPW / 597 / AAL08305 (A.t.)
Cell wall invertase / CIN / 3.2.1.26 / F – WAHSVS
R - WECPDF / 461 / AAM28822 (L.e.)
Galactokinase / GK / 2.7.1.6 / F – GGMDQA
R - TGAGWG / 701 / NP_187310 (A.t.)
Hexokinase / HK / 2.7.1.1 / F – DAMTVEM
R - MVINMEWG / 680 / AAG35735 (L.e.)
Fructokinase / FK / 2.7.1.4 / F – GAPANVA
R - DTTGAG / 674 / AAB57734 (L.e.)
Phosphoglucomutase, plastidic / PGMpl / 5.4.2.2 / F – SHNPGG
R - DPVDGS / 1092 / AAG44095 (A.t.)
Phosphoglucomutase, cytosolic / PGMcyt / 5.4.2.2 / F – ADGDAD
R - DPVDGS / 617 / CAB60127 (P.s.)
Phosphoglucose isomerase, plastidic / PGIpl / 5.3.1.9 / F – MVGHYW
R - HQPGVEA / 1171 / Q9SB57 (A.t.)
Phosphoglucose isomerase, cytosolic / PGIcyt / 5.3.1.9 / E – AFWDWV
R - DQWGVE / 742 / NP_199088 (A.t.)
UDPGlc/Gal PPase / UGGP / F – AGLRWV
R - EVEVWP / 687 / AAK25946 (A.t.)
Uridyltransferase / UT / 2.7.7.12 / F – EH/QE/QCAPE
R - NPVFPEDV / 825 / AAM64928 (A.t.)
UDPGlc PPase / UGP / 2.7.7.9 / F - TMGCTG
R - PKEVDG / 705 / AAB71613 (S t.)
UDPGlc epimerase / UGE / 5.1.3.2 / F – VIHFAG
R - DLADGH / 500 / BAC43316 (A.t.)
Sucrose synthase / SUS / 2.4.1.13 / F – AMNH/NADF
R - GAFVQP
F – ETGGQV
R - GAFVQP / 603
1120 / NP_197583 (A.t.)
Sucrose-P synthase / SPS / 2.4.1.14 / F – DTGGQV
R - GHYADAG
F - GQVAYP
R – RWGGEG / 389
1000 / NP_197528 (A.t.)
Supplementary Table 2: Comparison of expression of the sugar metabolism genes in fruit and non-fruit libraries in the ICuGI EST database ( version 3. The description of the different libraries comprising the datbase can be found at Genes which were cloned from mixed melon fruit cDNA using degenerate primers for conserved amino acid sequences are indicated by +.* indicates those genes cloned from gDNA. The fruit ESTs do not include the genes directly cloned from melon fruit cDNA which are listed in the database under library SSH9.
Enzyme Gene Direct cloning ESTs libraries
from cDNA (Total number of EST)
Fruit Flower Vegetative Callus
(34,374) (26,627) (43,725) (22,204)
Acid -galactosidase 1 / AAG1 / + / 0 / 1 / 2 / 3
Acid -galactosidase 2 / AAG2 / + / 0 / 0 / 0 / 0
Neutral -galactosidase 1 / NAG1 / + / 0 / 0 / 0 / 9
Neutral -galactosidase 2 / NAG2 / + / 5 / 3 / 3 / 4
Neutral -galactosidase 3 / NAG3 / 0 / 0 / 4 / 0
Acid invertase 1 / AIN1 / + / 0 / 0 / 0 / 0
Acid invertase 2 / AIN2 / +* / 0 / 0 / 0 / 1
Neutral invertase 1 / NIN1 / + / 0 / 0 / 3 / 0
Neutral invertase 2 / NIN2 / + / 0 / 0 / 1 / 0
Neutral invertase 3 / NIN3 / 1 / 0 / 1 / 8
Neutral invertase 4 / NIN4 / 0 / 0 / 1 / 0
Cell wall invertase 1 / CIN1 / 0 / 0 / 3 / 0
Cell wall invertase 2 / CIN2 / 0 / 0 / 1 / 2
Cell wall invertase 3 / CIN3 / 1 / 0 / 1 / 0
Cell wall invertase 4 / CIN4 / +* / 0 / 0 / 2 / 0
Invertase inhibitor1 / INH1 / 3 / 0 / 0 / 0
Invertase inhibitor2 / INH2 / 0 / 1 / 5 / 0
Invertase inhibitor3 / INH3 / 0 / 0 / 2 / 0
Galactokinase / GK / + / 2 / 1 / 2 / 7
Hexokinase 1 / HK1 / + / 0 / 0 / 0 / 0
Hexokinase 2 / HK2 / + / 0 / 0 / 1 / 4
Hexokinase 3 / HK3 / 1 / 0 / 0 / 0
Fructokinase 1 / FK1 / + / 0 / 0 / 1 / 0
Fructokinase 2 / FK2 / + / 0 / 0 / 2 / 0
Fructokinase 3 / FK3 / 2 / 0 / 1 / 24
Phosphoglucomutase (plastidic) / PGMpl / + / 2 / 0 / 5 / 1
Phosphoglucomutase (cytosolic) / PGMcyt / + / 0 / 0 / 3 / 5
Phosphoglucose
isomerase (plastidic) / PGIpl / + / 2 / 1 / 2 / 9
Phosphoglucose
isomerase (cytosolic) / PGIcyt / + / 0 / 0 / 3 / 5
UDPglc/gal pyrophosphorylase / UGGP / + / 1 / 1 / 0 / 4
Gal-1-P uridyltransferase / UT / +* / 0 / 0 / 2 / 0
UDPglc pyrophosphorylase / UGP / + / 2 / 0 / 4 / 4
UDPglc epimerase 1 / UGE1 / + / 5 / 2 / 3 / 10
UDPglc epimerase 2 / UGE2 / 1 / 0 / 0 / 0
UDPglc epimerase 3 / UGE3 / 2 / 0 / 0 / 0
Sucrose synthase 1 / SUS1 / + / 3 / 0 / 2 / 0
Sucrose synthase 2 / SUS2 / + / 1 / 0 / 1 / 0
Sucrose synthase 3 / SUS3 / 1 / 0 / 0 / 0
Sucrose-P synthase 1 / SPS1 / + / 4 / 0 / 1 / 2
Sucrose-P synthase 2 / SPS2 / 0 / 0 / 2 / 1
Sucrose-P phosphatase 1 / SPP1 / 2 / 0 / 1 / 0
Sucrose-P phosphatase 2 / SPP2 / 0 / 0 / 3 / 1
Supplemental Figure 1:
Fig.1SCluster analysis of gene expression profiles. Genes which did not cluster with others included GK and UGE2 and these are not presented. Figures A-E are genes downregulated during the sucrose accumulation phase and figures F-I are genes upregulated during the sucrose accumulation phase. Cluster analysis of melon gene expression was performed using a k-medoids clustering (Kaufman and Rousseeuw 1990). For these analyses expression values were standardized so that each profile had a mean of 0 and a standard deviation of 1. The number of clusters was determined using the gap statistic approach (Tibshirani et al. 2001). The cluster analysis and the outcome graphs were performed using R statistical software ( code available upon request).
Literature cited
Kaufman L, Rousseeuw PJ (1990) Finding groups in data: an introduction to cluster analysis. Wiley, New York.
Tibshirani R, Walther G, Hastie T (2001) Estimating the number of clusters in a data set via the gap statistic. J R Stat Soc Ser B Stat Methodol 63:411–423.