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Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato
Author(s) -
MingJung Liu,
Koichi Sugimoto,
Sahra Uygun,
Nicholas Panchy,
Michael S. Campbell,
Mark Yandell,
Gregg A. Howe,
ShinHan Shiu
Publication year - 2018
Publication title -
the plant cell
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 5.324
H-Index - 341
eISSN - 1532-298X
pISSN - 1040-4651
DOI - 10.1105/tpc.18.00194
Subject(s) - biology , domestication , gene , transcriptome , gene expression , regulation of gene expression , functional divergence , transcription factor , genetics , gene expression profiling , solanum , gene family , botany
The evolution of transcriptional regulatory mechanisms is central to how stress response and tolerance differ between species. However, it remains largely unknown how divergence in cis -regulatory sites and, subsequently, transcription factor (TF) binding specificity contribute to stress-responsive expression divergence, particularly between wild and domesticated species. By profiling wound-responsive gene transcriptomes in wild Solanum pennellii and domesticated S. lycopersicum , we found extensive wound response divergence and identified 493 S. lycopersicum and 278 S. pennellii putative cis -regulatory elements (pCREs) that were predictive of wound-responsive gene expression. Only 24-52% of these wound response pCREs (depending on wound response patterns) were consistently enriched in the putative promoter regions of wound-responsive genes across species. In addition, between these two species, their differences in pCRE site sequences were significantly and positively correlated with differences in wound-responsive gene expression. Furthermore, ∼11-39% of pCREs were specific to only one of the species and likely bound by TFs from different families. These findings indicate substantial regulatory divergence in these two plant species that diverged ∼3-7 million years ago. Our study provides insights into the mechanistic basis of how the transcriptional response to wounding is regulated and, importantly, the contribution of cis -regulatory components to variation in wound-responsive gene expression between a wild and a domesticated plant species.

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