Supporting Information
Table S1: Comparative analysis of AA metabolic genes distribution among tomato
chromosomes
The nucleotide sequence of each gene was blasted versus the whole tomato genome.
Chromosomes containing these genes were identified as listed.
Figure S1: Average correlation coefficient and network properties before and after
removal of TAAs in the background of the 2005 dataset
Shown are the results of the average correlation coefficient (ACC) and three network
properties: weighted node degree average, global clustering coefficient, and assortativity.
The ACC of the TAA cliques was compared to the ACC of the random cliques. The
network properties were analyzed after removal of the TAA cliques and random cliques.
All properties were measured for different stages of network manipulation, representing
the size of the cliques 3 to 6. E.g. the weighted node degree average was calculated after
the removal for all possible combinations of subgroups of the TAA clique of size 3 and
compared to the removal of all cliques in the network of size 3 not containing any TAAs.
P-values were estimated based on empirical p-value calculations, error bars represent
standard deviations.
Abbreviations used: met = metabolite/s; target AA = target amino acids;
“-” in front of met indicates removal of clique
Data S1: Glossary of network terminology
Definitions of network terms used in the manuscript.
Data S2: Comparative analysis of different community-detecting algorithms applied
Shown are the results of the different community-detecting algorithms (CDA) applied
(fast-greedy, walktrap, and edge-betweenness) to the 2004 seed metabolite network. For
each CDA different numbers of communities were imposed (3-23) with subsequent
analysis of the clustering of the TAAs and the residual nodes.
Data S3: Results of average correlation coefficient (ACC) analysis of the TAA cliques
and neighboring nodes
The magnitude of the ACC of the TAA clique was compared to the ACC of individual
TAAs to other adjacent nodes forming a clique of size 6. For each TAA, all cliques of
size 6 to other adjacent nodes were identified and the ACC estimated and compared to
the TAA clique ACC. The number of identified cliques was used for p-value estimations.
Data S4: Results of the GC-MS AAs metabolic analysis of the new grown tomato ILs of
chromosome 2 (season 2013/14).
Shown is the relative content of 18 amino acids for lines M82 (WT), 2-5, 2-5-1, 2-5-5, 25-6, 2-5-13, and 2-6-5 quantified by GC/MS from seeds grown in the greenhouse,
Midreshet Ben Gurion, Israel in 2013/14. Values were normalized by the fresh weight
and the internal standard ribitol.
Data S5: Amino acid alignments of candidate genes between M82 and S. pennellii
Alignments of predicted amino acid sequences of candidate genes described in the main
text between M82 and S. pennellii. Differences in sequences are color-highlighted.
Data S6: Alignment of SIFT predicted amino acid sequence of the two Proline
dehydrogenases between M82 and S. pennellii
Only for the two identified Proline dehydrogenases Sorting Tolerant From Intolerant
(SIFT) predictions, predicted differences in the coding region impacting enzyme
functionality. The alignment between M82 of and S. pennellii of the amino acid
sequences for the two Proline dehydrogenases are shown here.
Data S7: Summary of cross species alignment results of matching genes.
Listed are the identified candidate genes, summarizing the results originated from the
alignment between M82 and S. pennellii of the coding regions and ~1000 bp upstream
regions.
Data S8: Upstream region alignments of candidate genes between M82 and S. pennellii
Alignments of DNA nucleotide sequences upstream regions (~1000 bp) of candidate
genes described in the main text between M82 and S. pennellii.
Data S9: Summary of gene upstream region analysis, including transcription factor
binding site and tandem repeats.
Listed are the identified candidate genes with identified transcript factors and their
descriptions, and tandem repeats within the genes’ upstream regions (~1000 bp).
Data S10: Truth-table of all identified transcription factor binding sites and their
occurrence in upstream regions of genes of interest.
Truth-table listing the transcription factors binding sites corresponding to the
transcription factors described in Data S9 and their occurrence in the upstream regions of
the candidate genes described in the main text.
Data S11: Detailed analysis of RT-PCR, promoter regions, and transcription factor
binding sites
Detailed description of the experimental procedures applied for RNA extraction and
quantitative real-time PCR, analyses of coding and promoter regions complementing the
sections of the main text, titled: i) RNA extraction and quantitative real-time qPCR
analysis of gene expression levels; ii) Analysis of coding regions; and iii) Analysis of
promoter regions.