## 3 Discussion
During the downstream of the Hyp biosynthetic pathway in dark glands, most of the steps are catalyzed by the oxidation, reduction, dehydration and decarboxylic reactions, as well as free radical coupling and electron-paired donors (Figure 1). For example, flavonoid 3\({}^{\prime}\)-monooxygenase (CYP75B2) catalyzes the 3\({}^{\prime}\)-hydroxylation of flavonoid B-ring to a 3\({}^{\prime}\), 4\({}^{\prime}\)-hydroxylated state [48], isoflavene 2\({}^{\prime}\)-hydroxylase (CYP81E1) catalyzes the hydroxylation of isoflavones to 2\({}^{\prime}\)-hydroxyisoflavones, daidzein to 2\({}^{\prime}\)-hydroxydaidzein and formononetin to 2\({}^{\prime}\)-hydroxyformonentin [49]. The UR of genes that encode CYPs may play critical roles in Hyp biosynthesis in the downstream pathway. However, the genes involved in downstream steps (e.g., PKS, OKS, TER, POCP and BBE) were not examined to be differentially expressed, except for the CYPs class (Figure 1). While several studies were devoted to dissecting the Hyp biosynthetic pathway [9; 10; 11; 22; 24; 25; 26], limited genes involved in the downstream steps were submitted to the public databases (e.g., NR, Swiss-Prot, KEGG, KOG and GO), which led to differentially expressed contigs that could not be mapped and were listed as unidentified or uncharacterized genes in this study. Adaptation to environmental stresses results from integrated events occurring at all levels of organization, not only from the anatomical, cellular, biochemical and molecular levels but, also, from the morphological level [32]. For example, the alkane hydroxylase MAH1 (CYP96A15) is involved in wax biosynthesis during plant growth [50]. The Leucine-rich repeat receptor protein kinase (EMS1) can mediate signals that control the fate of reproductive cells and their contiguous somatic cells [51]. The GLABRA2 expression modulator (GEM) is involved in the spatial control of cell division and differentiation of root epidermal cells [52]. MIZU-KUSSEI 1 (MIZ1) plays an important role in lateral root development [53]. Subtilisin-like serine proteases (SBTI1.1) can promote plant cell differentiation, organogenesis and somatic embryogenesis, as well as cell proliferation [54]. Zeatin O-glucosyltransferase (ZOG1) catalyzes the formation of O-xylosylzeatin in plant development [55]. The differential expression of the 15 genes involved in the morphophysiological traits may be an adaptation to low temperatures. There is considerable evidence that HSPs are essential for plant survival under abiotic stresses [56; 57]. The expression of HSP genes is observed to be induced by high temperatures and inhibited by low temperatures [58; 59]. For example, CRPs are induced to enable plants to survive from chilling and freezing stress [60]. Three CRPs that were identified in this study--for example, BON1-associated protein 1 (BAP1), cold-regulated 413 inner membrane protein 1 (COR413 IM1) and cold-responsive protein kinase 1 (CRPK1)--were observed to be differentially expressed in response to cold stress [61; 62; 63]. TFs can regulate plant growth and metabolism in response to abiotic stresses [64]. For example, ethylene-responsive transcription factors (ERFs) are involved in regulating gene expression and participating in signal transduction pathways [65; 66]. MYB transcription factors play regulatory roles in developmental processes and defense responses, the MYB4 is involved in scavenging reactive oxygen species during cold stress [67] and MYB14 induces the expression of \(CBF\) genes to increase their freezing tolerance [68]. The NAC domain-containing protein family may act downstream of N-rich protein (NRP)-A or NRP-B in the integration of endoplasmic reticulum stress and osmotic stress cell death signals [69]. WRKY domain transcription factors play an important role in plant responses to both biotic and abiotic stress by regulating ABA signaling [70].