Figure 1.
Figure 1.

Comparison of frequency distribution of length of reads obtained by 454 pyrosequencing of two ‘Dulce’ 40-d rind (40R) libraries prepared using different protocols. A. Protocol A. B. Protocol B, which includes a purification step. Number of reads, mean length, and total yields are presented for each library. Mb, Mbp.

 


Figure 2.
Figure 2.

Length (A) and number of reads (B) of assembled contigs.

 


Figure 3.
Figure 3.

Heat-map analysis of correlations among 16 complementary DNA (cDNA) libraries sequenced by 454 technology and 10 cDNA libraries sequenced by traditional methods available at the International Cucurbit Genomics Initiative (ICuGI) database (version 2). The numbers in the cells are Pearson correlation coefficients between two samples. Color brightness is proportional to the correlation coefficient. Good correlation (bright red color) was found between sequences obtained by both sequencing methods from libraries of the same genotypes, tissues, and developmental stages.

 


Figure 4.Figure 4.
Figure 4.

Continued on next page. Comparison of expression patterns of selected genes as determined by 454 pyrosequencing (dark columns) and reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) (gray columns). A. Twenty genes upregulated in young fruit. B. Twenty genes upregulated in mature fruit. Transcript abundance in 454 libraries was measured by counting and the same complementary DNA (cDNA) libraries were analyzed by RT-qPCR. Both 454 digital expression values (ppm) and RT-qPCR relative expression ratio (R) values were normalized to the median across 14 samples for each gene. Gene expression was plotted as Log10 (y axis) of the 454 and RT-qPCR normalized values. X axis: Days after anthesis; rind (R) and flesh (F) tissues; genotypes: PI414723 and ‘Dulce’. Gene numbers and abbreviations are according to Table 3. Numbers in parentheses indicate similarity of expression patterns between the two methods, as determined by Pearson correlation.

 


Figure 5.
Figure 5.

Scatter-plot comparison of the expression level (Log10) of 40 genes by 454 pyrosequencing (x axis) and reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) (y axis). Correlation was based on 560 ratio points calculated for 40 genes across developmental stages, fruit tissues (rind and flesh), and two genotypes.