Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato
Regulatory Divergence in Wound-Responsive Gene Expression between Domesticated and Wild Tomato
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DOI：
10.1105/tpc.18.00194
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发表时间：
2018-07-01
期刊：
影响因子：
11.6
通讯作者：
Shiu, Shin-Han
中科院分区：
文献类型：
--
作者：
Liu, Ming-Jung;Sugimoto, Koichi;Shiu, Shin-Han
转录调控机制的进化是物种间应激反应和耐受性差异的核心。然而，它仍然在很大程度上是未知的分歧，顺式调控位点，随后，转录因子（TF）的结合特异性有助于应力响应的表达分歧，特别是野生和驯化物种之间。通过对野生龙葵和驯化龙葵的创伤反应基因转录组进行分析。在番茄中，我们发现了广泛的伤口反应分歧，并鉴定了493个S。lycopersicum和278 S. pennellii推定的顺式调节元件（pCREs），其预测创伤响应基因表达。只有24-52%的这些伤口反应pCREs（取决于伤口反应模式）在跨物种的伤口反应基因的推定启动子区域中一致富集。此外，在这两个物种之间，它们在pCRE位点序列上的差异与伤口反应基因表达的差异显著正相关。此外，类似于11-39%的pCREs仅特异于一种物种，并且可能与来自不同科的TF结合。这些发现表明，这两种植物物种在300万至700万年前发生了巨大的调节分歧。我们的研究提供了深入了解创伤的转录反应是如何调节的机制基础，重要的是，顺式调节成分的贡献，在野生和驯化的植物物种之间的伤口响应基因表达的变化。
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, similar to 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 similar to 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.