Fraxinus mandshurica (Manchurian ash) is an ecologically and economically valuable hardwood tree native to Northeast Asia, yet its genomic resources remain limited. We assembled its complete chloroplast (cp) genome (155,559 bp) using hybrid PacBio and Illumina sequencing and performed comparative, phylogenetic, and evolutionary analyses. The cp genome exhibits a typical quadripartite structure encoding 132 gene copies, comprising 114 unique genes (80 protein-coding, 30 tRNA, and 4 rRNA genes), with 18 genes duplicated in the inverted repeat (IR) regions. Simple sequence repeat analysis revealed dominance of mononucleotide A/T repeats. Phylogenetic analysis of 53 complete cp genomes strongly supported the monophyly of Oleaceae and resolved F. mandshurica as sister to the North American F. nigra, consistent with previously proposed Miocene intercontinental dispersal scenarios between East Asia and North America. Most protein-coding genes were under strong purifying selection (Ka/Ks << 1), whereas petB, rpl2, and several ndh genes showed elevated Ka/Ks values that are suggestive of altered selective constraint but are based on very few substitutions and are therefore not, on their own, evidence of positive selection. Nucleotide diversity (Pi) analysis identified 15 hypervariable intergenic spacers (mean Pi = 0.067), among which trnM-CAU-rps14, ndhJ-ndhK, and petL-petG represent promising candidate barcode regions requiring further validation. This study provides a high-quality, fully annotated cp genome of F. mandshurica and a valuable genomic resource for future phylogenetic, population genetic, and conservation studies of this important genus.

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.