DOI: 10.5061/dryad.8cz8w9gzh
title: Data for: Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster

description: Tremendous plant metabolic diversity arises from
 phylogenetically-restricted specialized metabolic pathways. Specialized
 metabolites are synthesized in dedicated cells or tissues, with pathway
 genes sometimes colocalizing in biosynthetic gene clusters (BGCs).
 However, the mechanisms by which spatial expression patterns arise and the
 role of BGCs in pathway evolution remain underappreciated. In this study,
 we investigated the mechanisms driving acylsugar evolution in the
 Solanaceae. Previously thought to be restricted to glandular trichomes,
 acyl sugars were recently discovered in cultivated tomato roots. We
 demonstrated that acyl sugars in cultivated tomato roots and trichomes
 have different sugar cores, identified root-enriched paralogs of trichome
 acyl sugar pathway genes, and characterized a key paralog required for
 root acyl sugar biosynthesis, SlASAT1-LIKE (SlASAT1-L), which is nested
 within a previously-reported trichome acyl sugar BGC. Finally, we provided
 evidence that ASAT1-L arose through duplication of its paralog, ASAT1, and
 was trichome-expressed before acquiring root-specific expression in the
 Solanum genus. Our results illuminate the genomic context and molecular
 mechanisms underpinning metabolic diversity in plants.
description: # **Data for: Tomato root specialized metabolites evolved through gene
 duplication and regulatory divergence within a biosynthetic gene cluster**
 [https://doi.org/10.5061/dryad.8cz8w9gzh](https://doi.org/10.5061/dryad.8cz8w9gzh) This dataset consists of Table S2 from Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster. ## **Description of the data and file structure** Table S2 summarizes results from differential gene expression analysis and weighted gene coexpression analysis (WGCNA) of 274 publicly available cultivated tomato (Solanum lycopersicum) transcriptome samples, representing 84 tissue-developmental stage sample groups. Table S2 contains 125 columns and 26,364 rows, with results from each gene expressed across the 84 tissue-developmental stage groups (26,364 of 34,620 annotated genes were expressed in our dataset). The WGCNA coexpression network module that each gene falls into is listed in column one. The name, description, and genomic position of each gene are listed in columns two to seven. Columns eight to 41 summarize results from differential gene expression analyses, including relative transcript abundance as log2 adjusted fold-change (adjFC) and multiple-test corrected p-value for each pairwise comparison. Columns 42 to 125 list absolute expression abundance in transcripts per million (TPM) for each of the 84 tissue-developmental stage sample groups. For details on each transcriptome sample, please refer to Table S1 of “Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster”. For details on differential gene expression analysis and WGCNA, please refer to the methods documented in “Tomato root specialized metabolites evolved through gene duplication and regulatory divergence within a biosynthetic gene cluster”.