Understanding the genetic basis for changes in transcriptional regulation is an important aspect of understanding phenotypic evolution. Using interspecific introgression lines, we infer the mechanisms of divergence in genome-wide patterns of gene expression between the nightshades Solanum pennellii and S. lycopersicum (domesticated tomato). We find that cis- and trans-regulatory changes have had qualitatively similar contributions to divergence in this clade, unlike results from other systems. Additionally, expression data from four tissues (shoot apex, ripe fruit, pollen, and seed) suggest that introgressed regions in these hybrid lines tend to be down-regulated, while background (non-introgressed) genes tend to be up-regulated. Finally, we find no evidence for an association between the magnitude of differential expression in NILs and previously determined sterility phenotypes. Our results contradict previous predictions of the predominant role of cis- over trans-regulatory divergence between species, and do not support a major role for gross genome-wide misregulation in reproductive isolation between these species. R source, markdown and helper fileThe zip file contains all the source code used in our study (Guerrero_etal_source.R), as well as the R markdown file (Guerrero_etal_SuppInfo.Rmd) used to produce the Supporting Information (the .pdf output is also included). Two more files necessary for running the scripts (isNIL_bool_*) are included. These have the information on the state of each gene in the S. lycopersicum genome with respect to the introgressed regions in each introgression line. An allele can be introgressed (coded "true") or background (coded "false")Guerrero_etal_scripts.zipAnther (pollen) gene expression dataGene expression in pollen (microarray data) for 4 S. lycopersicum x S. pennellii introgression lines, and for S. lycopersicum. Protocols described in the GEO entry.Carpel (seed) gene expression dataGene expression in seed (from microarrays) for 3 S. lycopersicum x S. pennellii introgression lines, and for S. lycopersicum. Protocols described in the GEO entry.Gene expression in vegetative tissueProcessed data generated from RNA-Seq data from apices of 74 S. lycopersicum x S. pennellii introgression lines, and the two parents, from Chitwood et al. (2013; The Plant Cell, 25). Please see Readme.txt for further details on how to obtain the raw data.Leaf_sun_expression.txt