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Data obtained from two libraries prepared twice from the same poly(A)+ messenger (mRNA) sample (Dulce 40 flesh).

 
Libraries Mbp Reads Mean length, bp
Dulce 40F A 11.99 64,963 185
Dulce 40F B 11.87 60,398 196
40F, 40-d flesh.



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Summary statistics for clustering data relating to melon database and distribution between genotypes and tissues.

 
Consideration Contigs % Reads % Contigs† %
A. Sizes of contigs
Singletons 32,357 48.0 32,357 2.8
Nonsingletons 35,120 52.0 1,118,300 97.2
Large contigs (>10 reads) 13,418 19.9 1,038,774 90.3 13,416 100
Total 67,477 100 1,150,657 100 13,418 100
B. 454 contigs mapped to ICuGI melon database
Contigs aligning to melon database 11,093 16.4 886,004 77.0 8619 64.2
454 contigs only 54,700 81.1 262,510 22.8 4797 35.8
Melon ICuGI database only 1684 2.5 2143 0.2 2 0.0
Total 67,477 100 1,150,657 100 13,418 100
C. Distribution of genotypes in 454
Contigs of PI414723 and ‘Dulce’ 24,610 37.4 1,084,362 94.4 13,173 98.2
Contigs of PI414723 only 15,786 24.0 24,199 2.1 101 0.8
Contigs of ‘Dulce’ only 25,397 38.6 39,953 3.5 142 1.1
Total 65,793 100 1,148,514 100 13,416 100
D. Distribution of fruit tissues in 454
Contigs of rind and flesh 24,879 37.8 1,081,470 94.2 13,098 97.6
Contigs of rind only 21,681 33.0 39,526 3.4 244 1.8
Contigs of flesh only 19,233 29.2 27,518 2.4 74 0.6
Total 65,793 100 1,148,514 100 13,416 100
Large contigs are included in the nonsingletons.
ICuGI, International Cucurbit Genomic Initiative; database available at http://www.icugi.org (verified 10 Jan. 2011), version2.



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List of genes showing differential expression based on read counts in 454 libraries of PI414723 and ‘Dulce’ and used for validation of expression quantification.

 
Accession no. Gene or enzyme 454 reads PC Abbreviation
A. Genes upregulated in young fruits
1 AF230211 Translationally controlled tumor protein 4136 0.86 TCTP
2 DQ288986 Alcohol dehydrogenase 3696 0.91 ADH 1
3 AM723137 Catalase isozyme 3 3131 0.87 CAT3
4 EB715472 HyPRP2 2633 0.94 HyP
5 EB715966 No hits found 2584 0.84
6 AF436852 Pyruvate decarboxylase 2509 0.88 PDC
7 DV632484 Ribulose bisphosphate carboxylase 2393 0.79 RBCS
8 DV634533 Glyceraldehyde-3-phosphate dehydrogenase 2041 0.77 GPDH
9 DV634305 Chlorophyll a/b-binding protein 1685 0.91 CAB1
10 DV634171 Dehydrin 1515 0.81 DEH
11 DV632443 Lipid transfer protein isoform 4 1473 0.91 LTP
12 DV634731 Polyubiquitin 10 1450 0.46 UBQ10
13 DV634376 Chlorophyll a/b-binding protein 1033 0.90 CAB2
14 DV632050 Elongation factor 1-alpha 896 0.41 EF1A
15 DV633092 Vacuolar cation/proton exchanger 1a 739 0.88 CAX
16 DV634937 Elongation factor 1-gamma 513 0.64 EF1B
17 AM718345 Clathrin heavy chain 349 0.50 Clathrin
18 DQ267934 13S-lipoxygenase 235 0.73 LOX1
19 DV634569 Hypothetical protein 106 0.53 OR1
20 DV634330 RNA-binding protein 26 0.70 RRM
B. Genes upregulated in mature fruits
21 DV633682 Adenosylhomocysteinase 4327 0.87 SAHH
22 X69935 ACC oxidase 4152 0.98 ACO1
23 AF426403 Abscisic acid response protein 4019 0.95 ASR1
24 DV632379 Type-2 metallothionein 3159 0.92 Type-2 MT
25 Z70522 Major latex protein 2996 0.94 pMEL7
26 DV632508 Branched-chain-amino-acid transaminase 2994 0.93 BCAT
27 DV633298 No hits found 2788 0.88
28 DV633532 Stearoyl-acyl carrier protein desaturase 2666 0.99 DES
29 DV632631 Acyl carrier protein 2458 0.93 ACP
30 DV634049 ECERIFERUM 1, octadecanal decarbonylase 1921 0.94 CER1
31 Z70521 Alcohol acetyltransferase 1753 0.94 AAT1
32 DV633593 Glutathione S-transferase 1411 0.92 GST
33 DV633781 Beta-1,3-glucanase 1186 0.88 BG
34 DV632686 Expansin 941 0.92 EXP1
35 DV631909 Ripening-related protein grip22 861 0.87 Kiw
36 DV634429 Sucrose-phosphate synthase 1 417 0.70 SPS1
37 DV632450 No hits found 192 0.86
38 DV633411 UDP-glucose 4-epimerase 1 173 0.68 UGE1
39 DV633715 Acireductone dioxygenase 59 0.65 ARD4
40 DV632398 No hits found 47 0.75
PC, Pearson correlation: between Log10 reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) and Log10 454 pyrosequencing expression level.
RNA, ribonucleic acid.