Table 1.
Measured phytochemical concentration of red ripe tomato fruit.
Soluble solids, total phenolics (gallic acid equivalents, GAE), lycopene, total Trolox equivalent antioxidant capacity (TTEAC), lypophilic TEAC, hydrophilic TEAC, and reduced ascorbic acid concentrations on fresh weight (FW) and dry weight (DW) bases (except soluble solids) under conventional (CONV) and organic (ORG) fertilizer treatments. Data were analyzed using SAS Mixed Model. (See Supplementary file for measured observations, LS means, standard deviation, and standard error).
Fig 1.
Representative ORG and CONV log10 RPKM ratio Manhattan plot representations of expression values across S. lycopersicum chromosomes.
Every bar is indicative of the log10 expression ratio of Fruit and Leaf ORG RPKM values over Fruit and Leaf CONV RPKM values. Trendlines with slope equations indicate propensity of treatment activated loci across the chromosome. Chromosome graph lengths are not indicative of chromosome length. Red bars indicate a higher log10 ratio in the CONV treatment and blue bars indicate higher expression in the ORG treatment at any given position on the chromosome. Trend lines were graphed to indicate a predominance of chromosomal activity either in the ORG treatment (positive y-intercept value) or in the CONV treatment (negative y-intercept value). All 12 mapped chromosomes can be found in S3 Fig. 12 read files, representing three cDNA libraries across each of the two tissue and two treatment types were used for mapping purposes.
Fig 2.
Mean expression profile of the Lycopene pathway committed steps and significant differential enzymes.
PSY1 is the rate limiting step in the carotenoid biosynthesis pathway and the absence of LβCYC in the pathway increases the pool of lycopene from the pathway. A. psy1 RPKM expression values. B. Lβcyc1 RPKM expression values. C. psy1 leaf expression values with a different y-axis to discern standard error differences. D. Z-ISO leaf expression values. Table of annotations and accession numbers from Sol Genomics ITAG3.2. Error bars denote the standard error of sequenced expression values between 3 biological replicates.
Fig 3.
Mean expression profile of significant ascorbate pathway enzymes.
GGP1 and GMP1 are involved in the production of ascorbate (Smirnoff-Wheeler Pathway). APX.1, APX.2, SOD Cu-Zn.1, GSR2 and DHAR.1 are involved in the activation of ascorbate (Foyer-Halliwell-Asada Pathway). Table of annotations and accession numbers from Sol Genomics ITAG3.2. Additional ascorbate pathway gene expression can be found in S5 and S6 Figs. Error bars denote the standard error of sequenced expression values between 3 biological replicates.
Fig 4.
Gene Ontology Fisher’s Blast2GO analysis and queried with fruit tissues.
A. Biological Process gene ontology terms over represented in the ORG treatment compared to CONV treatment. B. Over represented Cellular Components in the ORG treatment versus the CONV treatment. C. Cellular Component ontology terms under represented in the ORG treatment compared to the CONV treatment. Size of slices represent ratio of numbers of contigs to total number of contigs in the represented categories.
Fig 5.
Expression profile of mean RPKM values of Nitrate Assimilation components in Fruit and Leaf tissue.
A. RPKM and RT-qPCR values for Nitrate Reductase. B. Low affinity nitrate transporters NRT1-2-11 and NRT1-4-6 C & D. RT-qPCR expression values for the highest expressed low and high affinity nitrate transporters. E. High affinity nitrate transporters NRT2-1.2, NRT2-1.1. RT-qPCR results (A, C and E) are averages of the number of replicates (N) and bars indicate the standard deviation between replicates. Table of annotations and accession numbers from Sol Genomics ITAG3.2. RT-qPCR relative values for tissue type and treatment, trend with the corresponding RPKM values generated from the HTS analysis. Error bars denote the standard deviation of RT-qPCR expression values between 3 biological replicates and at least 3 technical replicates. Error bars denote the standard error of sequenced expression values between 3 biological replicates.
Fig 6.
Expression profile of mean RPKM values of Nitrite Assimilation components in Fruit and Leaf tissue.
A. Chloroplast isoform of glutamine synthetase (cpGS) and glutamate synthase (GOGAT) RPKM and ΔΔCq values. B. RPKM values for two isoforms of Nitrate Reductase (nii1 and NiR) C. Identified homolog of plastidial nitrite transporter (NITR2). D. RPKM values for cytosolic isoform 1 of glutamine synthetase. Table of annotations and accession numbers from Sol Genomics ITAG3.2. Error bars denote the standard error of sequenced expression values, or in the case of cpGS and GOGAT RT-qPCR ΔΔCq values, between 3 biological replicates and at least 3 technical replicates.
Fig 7.
Differential expression of isocitrate lyase homologs.
A. Mean expression values for the identified isocitrate lyase isoforms. B. Table of annotations and accession numbers from Sol Genomics ITAG3.2. Error bars denote the standard error of sequenced expression values between 3 biological replicates.
Fig 8.
Mean RPKM expression values of enzymes involved in photosynthetic and/or tricarboxylic acid cycle respiratory pathway genes.
Table of annotations and accession numbers from Sol Genomics ITAG3.2. Error bars denote the standard error of sequenced expression values between 3 biological replicates.