###### Abstract  
Global development has generated a plethora of unfavorable and adverse environmental factors for the living organisms in the ecosystem. Plants are sessile organisms, and they are crucial to sustain life on earth. Since plants are sessile, they face a great number of environmental challenges related to abiotic stresses, such as temperature fluctuation, drought, salinity, flood and metal contamination. Salinity and drought are considered major abiotic stresses that negatively affect the plants' growth and production of useful content. However, plants have evolved various molecular mechanisms to increase their tolerance to these environmental stresses. There is a whole complex system of communication (cross-talk) through massive signaling cascades that are activated and modulated in response to salinity and drought. Secondary metabolites are believed to play significant roles in the plant's response and resistance to salinity and drought stress. Until recently, attempts to unravel the biosynthetic pathways were limited mainly due to the inadequate plant genomics resources. However, recent advancements in generating high-throughput \"omics\" datasets, computational tools and functional genomics approach integration have aided in the elucidation of biosynthetic pathways of many plant bioactive metabolites. This review gathers comprehensive knowledge of plants' complex system that is involved in the response and resistance to salinity and water deficit stresses as abiotic stress. Additionally, it offers clues in determining the genes involved in this complex and measures its activity. It covers basic information regarding the signaling molecules involved in salinity and drought resistance and how plant hormones regulate the cross-talking mechanism with emphasis on transcriptional activity. Moreover, it discusses many studies that illustrate the relationship between salinity and drought and secondary metabolite production. Furthermore, several transcriptome analysis research papers of medicinal plants are illustrated. The aim of this review is to be a key for any researcher that is aspiring to study the relationship between salinity and drought stresses and secondary metabolite production at the transcriptome and transcription level. salinity; drought; abiotic stress; phytohormones; ROS; signal transduction; cross-talk; secondary metabolite; transcriptome analysis +
Footnote †: journal: Applied Sciences  
lower levels of irrigation. On the contrary, abiotic stresses also have negative effects on the development and growth of the plant. For example, they can result in changing the reactive oxygen species (ROS) levels in the body and cause damage; these changes will force the plant to undergo programmed cell death (PCD) [4]. Other examples of negative effects of abiotic stresses are the osmotic and ionic stresses that occur when plants are exposed to increased levels of salinity and water shortage [5]. The plants tend to adapt to those abiotic stresses in order to survive and thrive [6]. There are many players that contribute to the process of resistance, including signaling molecules, DNA-binding proteins and an enormous number of stress-inducible genes. Those biological players participate in the complex orchestration of the plants' tolerance to stress at the molecular level. Stress-related molecules such as abscisic acid (ABA), jasmonic acid (JA) [7], ROS, calcium ions, a variety of transcription factors (TFs) and other regulatory and functional proteins all interact together in a spectacular manner in order to perform a remarkable adaptation to the abiotic stresses [8; 9]. This communication between secondary messengers, phytohormones, DNA-binding proteins and stress-inducible genes is known as \"cross-talk\" [9; 10]. In response to abiotic stresses, such as salinity and drought, the genetic regulation also involves a complex organization of metabolic activities that involve the intracellular production of beneficial secondary metabolites.