PT  - JOURNAL ARTICLE
AU  - Ming-Jung Liu
AU  - Koichi Sugimoto
AU  - Sahra Uygun
AU  - Nicholas Panchy
AU  - Michael S. Campbell
AU  - Mark Yandell
AU  - Gregg A. Howe
AU  - Shin-Han Shiu
TI  - Regulatory divergence in wound-responsive gene expression in domesticated and wild tomato
AID  - 10.1101/123992
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 123992
4099  - http://biorxiv.org/content/early/2017/04/04/123992.short
4100  - http://biorxiv.org/content/early/2017/04/04/123992.full
AB  - Background The evolution of cis- and trans-regulatory components of transcription is central to how stress response and tolerance differ across species. However, it remains largely unknown how divergence in TF binding specificity and cis-regulatory sites contribute to the divergence of stress-responsive gene expression between wild and domesticated species.Results Using tomato as model, we analyzed the transcriptional profile of wound-responsive genes in wild Solanum pennellii and domesticated S. lycopersicum. We found that extensive expression divergence of wound-responsive genes is associated with speciation. To assess the degree of trans-regulatory divergence between these two species, 342 and 267 putative cis-regulatory elements (pCREs) in S. lycopersicum and S. pennellii, respectively, were identified that were predictive of wound-induced gene expression. We found that 35-66% of pCREs were conserved across species, suggesting that the remaining proportion (34-65%) of pCREs are species specific. This finding indicates a substantially higher degree of trans-regulatory divergence between these two plant species, which diverged ∼3-7 million years ago, compared to that observed in mouse and human, which diverged ∼100 million years ago. In addition, differences in pCRE sites were significantly associated with differences in wound-responsive gene expression between wild and domesticated tomato orthologs, suggesting the presence of substantial cis-regulatory divergence.Conclusions Our study provides new insights into the mechanistic basis of how the transcriptional response to wounding is regulated and, importantly, the contribution of cis- and trans-regulatory components to variation in wound-responsive gene expression during species domestication.