Phenylalanine ammonia-lyase (PAL) serves as a pivotal regulatory enzyme at the initial branching point of the phenylpropanoid pathway, exerting a profound influence on downstream reactions essential for flavonoid biosynthesis. Glycyrrhiza species are important medicinal plants and provide plenty of roots as raw materials for further utilization, with the components of glycyrrhizic acid and flavonoids as two major active ingredients. However, functional studies of the PAL genes in the medicinal Glycyrrhiza species remain limited. In this study, we identified seven PAL family genes from each of the three medicinal Glycyrrhiza species, Glycyrrhiza uralensis Fisch., G. inflata Bat., and G. glabra L., and comprehensively analyzed their phylogenetic relationships, gene structures, motif distributions, and promoter cis-elements. Gene expression profiling revealed that PAL1 is highly expressed in roots and significantly induced by drought and salt stresses. We further selected G. uralensis GuPAL1 for functional investigation in Arabidopsis. GuPAL1-overexpression lines (GuPAL1-OE) demonstrated significant enhancements in plant growth, flavonoid accumulation, and hormone levels in Arabidopsis thaliana. Conversely, the Atpal1 mutant plants displayed marked reductions in these traits, while the transgenic lines of GuPAL1-OE in the Atpal1 mutant (Atpal1/GuPAL1) recovered to the normal phenotypes similar to wild type (WT). Transcriptomic analysis of the GuPAL1-OE plants compared to WT demonstrated that several key genes in the phenylpropanoid and flavonoid metabolic pathways (4CL, CCoAOMT, CAD, POD, F3H, FLS) were significantly enriched, suggesting that GuPAL1 may promote plant growth and flavonoid biosynthesis by regulating diverse cellular functions, metabolic pathways, and associated gene expressions. These findings highlight the functional importance of GuPAL1 in flavonoid biosynthesis, and provide valuable insights into the molecular mechanisms underlying the medicinal properties of Glycyrrhiza species.

Brown cotton is a major cultivar of naturally colored cotton, and brown cotton fibers (BCFs) are widely utilized as raw materials for textile industry production due to their advantages of being green and dyeing-pollution-free. However, the mechanisms underlying the pigmentation in fibers are still poorly understood, which significantly limits their extensive applications in related fields. In this study, we conducted a multidimensional comparative analysis of the transcriptomes and metabolomes between brown and white fibers at different developmental periods to identify the key genes and pathways regulating the pigment deposition. The transcriptomic results indicated that the pathways of flavonoid biosynthesis and phenylpropanoid biosynthesis were significantly enriched regulatory pathways, especially in the late development periods of fiber pigmentation; furthermore, the genes distributed in the pathways of PAL, CHS, F3H, DFR, ANR, and UFGT were identified as significantly up-regulated genes. The metabolic results showed that six metabolites, namely (−)-Epigallocatechin, Apiin, Cyanidin-3-O-glucoside, Gallocatechin, Myricetin, and Poncirin, were significantly accumulated in brown fibers but not in white fibers. Integrative analysis of the transcriptomic and metabolomic data demonstrated a possible regulatory network potentially regulating the pigment deposition, in which three MYB transcription factors promote the expression levels of flavonoid biosynthesis genes, thereby inducing the content increase in (−)-Epigallocatechin, Cyanidin-3-O-glucoside, Gallocatechin, and Myricetin in BCFs. Our findings provide new insights into the pigment deposition mechanism in BCFs and offer references for genetic engineering and breeding of colored cotton materials.