Acer triflorum Komarov is an important ornamental tree, and its seasonal change in leaf color is the most striking feature. However, the quantifications of anthocyanin and the mechanisms of leaf color change in this species remain unknown. Here, the combined analysis of metabolome and transcriptome was performed on green, orange, and red leaves. In total, 27 anthocyanin metabolites were detected and cyanidin 3-O-arabinoside, pelargonidin 3-O-glucoside, and peonidin 3-O-gluside were significantly correlated with the color development. Several structural genes in the anthocyanin biosynthesis process, such as chalcone synthase (CHS), flavanone 3-hydroxylase (F3H), and dihydroflavonol 4-reductase (DFR), were highly expressed in red leaves compared to green leaves. Most regulators (MYB, bHLH, and other classes of transcription factors) were also upregulated in red and orange leaves. In addition, 14 AtrMYBs including AtrMYB68, AtrMYB74, and AtrMYB35 showed strong interactions with the genes involved in anthocyanin biosynthesis, and, thus, could be further considered the hub regulators. The findings will facilitate genetic modification or selection for further improvement in ornamental qualities of A. triflorum.

Low temperature is an important environmental factor that affects the growth and development of trees and leads to the introduction of failure in the genetic improvement of trees. Acer pseudosieboldianum is a tree species that is well-known for its bright red autumn leaf color. These trees are widely used in landscaping in northeast China. However, due to their poor cold resistance, introduced A. pseudosieboldianum trees suffer severe freezing injury in many introduced environments. To elucidate the physiological indicators and molecular mechanisms associated with freezing damage, we analyzed the physiological indicators and transcriptome of A. pseudosieboldianum, using kits and RNA-Seq technology. The mechanism of A. pseudosieboldianum in response to freezing stress is an important scientific question. In this study, we used the shoots of four-year-old A. pseudosieboldianum twig seedlings, and the physiological index and the transcriptome of A. pseudosieboldianum under low temperature stress were investigated. The results showed that more than 20,000 genes were detected in A. pseudosieboldianum under low temperature (4 °C) and freezing temperatures (−10 °C, −20 °C, −30 °C, and −40 °C). There were 2505, 6021, 5125, and 3191 differential genes (DEGs) between −10 °C, −20°C, −30°C, −40 °C, and CK (4 °C), respectively. Among these differential genes, 48 genes are involved in the MAPK pathway and 533 genes are involved in the glucose metabolism pathway. In addition, the important transcription factors (MYB, AP2/ERF, and WRKY) involved in freezing stress were activated under different degrees of freezing stress. A total of 10 sets of physiological indicators of A. pseudosieboldianum were examined, including the activities of five enzymes and the accumulation of five hormones. All of the physiological indicators except SOD and GSH-Px reached their maximum values at −30 °C. The enzyme activity of SOD was highest at −10 °C, and that of GSH-Px was highest at −20 °C. Our study is the first to provide a more comprehensive understanding of the differential genes (DEGs) involved in A. pseudosieboldianum under freezing stress at different temperatures at the transcriptome level. These results may help to clarify the molecular mechanism of cold tolerance of A. pseudosieboldianum and provide new insights and candidate genes for the genetic improvement of the freezing tolerance of A. pseudosieboldianum.

Eleutherococcus senticosus, a medicinally important woody plant, is widely used in pharmaceuticals and functional foods due to its bioactive compounds. Its wild populations are facing severe threats due to over-harvesting. To inform scientific conservation and sustainable utilization strategies, this study aimed to comprehensively assess its genetic background. We developed 13 highly polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers from full-length transcriptome data, with an average polymorphism information content (PIC) of 0.52. Using these markers, we systematically evaluated the genetic diversity of 405 individuals from 22 natural populations across Northeast China. The results indicate that E. senticosus maintains moderate genetic diversity at the species level (mean expected heterozygosity He = 0.43), but substantial variation exists among populations. The Linjiang population showed the highest diversity (He = 0.58), whereas peripheral populations such as Tonghua (He = 0.31) and Huinan (He = 0.32) exhibited lower diversity. Analysis of molecular variance (AMOVA) revealed that genetic variation primarily resided within populations (66.3%), but moderate differentiation among populations was also detected (Fst = 0.21). Both structure analysis and clustering consistently divided all populations into two major genetic lineages. Frequent gene flow (e.g., Nm > 10 between Raohe and Hulin) and high genetic homogeneity were observed among populations in the core distribution area (e.g., Raohe, Jixi, Hulin), whereas several peripheral populations displayed significant genetic distinctiveness and isolation. This study provides the first macro-scale insight into the population genetic structure of E. senticosus, offering crucial molecular tools and a scientific basis for in situ and ex situ conservation, core collection establishment, and future genetic improvement of this species.