Ginkgo biloba L. is a well-known relict tree species and an important medicinal plant. Ginkgo is rich in secondary metabolites (SMs), mainly including flavonoids, lactones, and ginkgolic acid. The aim of this study was to determine variations in the concentrations of these SMs in Ginkgo leaves from different geographical populations. The SMs in the leaves of 298 clones from 10 geographical populations grafted under the same conditions were extracted and measured by high performance liquid chromatography (HPLC). The results showed that there were significant differences in concentrations of SMs in leaves from different populations (p < 0.01). The concentrations of both flavonoids and lactones were significantly negatively correlated with that of ginkgolic acid. Altitude and annual rainfall were important factors influencing the concentrations of lactones, and the frost-free period influenced the concentration of isorhamnetin. Population Yingdianjie (YDJ) was ideal for the plantations from which medicinal flavonoids and lactones are extracted, followed by populations Xiaopu (XP), Anlu (AL) and Wuchuan (WC). As variations within each population were found, attention should be paid to selection within populations.

Cherries (Prunus Subgenus Cerasus) have economic value and ecological significance, yet their phylogeny, geographic origin, timing, and dispersal patterns remain challenging to understand. To fill this gap, we conducted a comprehensive analysis of the complete chloroplast genomes of 54 subg. Cerasus individuals, along with 36 additional genomes from the NCBI database, resulting in a total of 90 genomes for comparative analysis. The chloroplast genomes of subg. Cerasus exhibited varying sizes and consisted of 129 genes, including protein-coding, transfer RNA, and ribosomIal RNA genes. Genomic variation was investigated through InDels and SNPs, showcasing distribution patterns and impact levels. A comparative analysis of chloroplast genome boundaries highlighted variations in inverted repeat (IR) regions among Cerasus and other Prunus species. Phylogeny based on whole-chloroplast genome sequences supported the division of Prunus into three subgenera, I subg. Padus, II subg. Prunus and III subg. Cerasus. The subg. Cerasus was subdivided into seven lineages (IIIa to IIIg), which matched roughly to taxonomic sections. The subg. Padus first diverged 51.42 Mya, followed by the separation of subg. Cerasus from subg. Prunus 39.27 Mya. The subg. Cerasus started diversification at 15.01 Mya, coinciding with geological and climatic changes, including the uplift of the Qinghai–Tibet Plateau and global cooling. The Himalayans were the refuge of cherries, from which a few species reached Europe through westward migration and another species reached North America through northeastward migration. The mainstage of cherry evolution was on the Qing–Tibet Plateau and later East China and Japan as well. These findings strengthen our understanding of the evolution of cherry and provide valuable insights into the conservation and sustainable utilization of cherry’s genetic resources.

As a widely used medicinal plant, Dendrobium loddigesii Rolfe is always a possible target for fraudulent labeling. The identification of D. loddigesii is generally difficult from its morphological and chemical appearance only. In order to develop a convenient and efficient identification method for D. loddigesii, six pairs of diagnostic ARMS primers were designed based on nrDNA ITS sequences of D. loddigesii and eleven adulterants. The results showed that one diagnostic primer pair (FJB-04-forward, FJB-04-reverse) could be used to authenticate D. loddigesii by generating a fragment of 353 bp at annealing temperatures from 48 °C to 62 °C while the other diagnostic primer pair (FJB-03-forward, FJB-03-reverse) took on the same effect at annealing temperatures from 49 °C to 55 °C. This points out the potential of ARMS analysis for authentication of D. loddigesii.

Ginkgo biloba L., as one of the oldest tree species, is a very important medicinal plant due to the metabolites in its leaves. To explore the variations and genetic regulation of leaf phenotypic traits, 321 samples from 12 ancient populations in the major distribution areas in China were collected for the leaf morphometric analysis, and 126 samples from 9 ancient populations were used for the genome-wide association study (GWAS) of leaf traits. The results showed that the leaf weight (fresh weight and dry weight) and size (areas) varied greatly, while the length:width ratio (LWR) was stable. There were significant differences in leaf traits among different ancient populations (p < 0.01), and population ZJ from eastern China—with a greater leaf weight and size—was ideal for leaf production. Leaf thickness (LT) showed correlations with altitude, longitude and frost-free period, while LWR had a correlation with altitude (p < 0.05). However, the correlations between environmental factors and leaf traits were weak, which may be related to the origin of populations and human activities. A GWAS revealed that 29 single nucleotide polymorphism (SNP) loci and 112 candidate genes related to leaf traits, and Gb_04106, which is related to auxin, may be involved in the genetic regulation of LT. It is speculated that environmental factors may induce leaf morphology of G. biloba by affecting the accumulation of secondary metabolites. The results of this study may provide a theoretical basis for studying the variation pattern and genetic regulation of leaf phenotypes.

Triadica sebifera (Linnaeus) Small is a tree species native to China. The seeds of T. sebifera are rich in oil and are widely used in industrial fields. To explore the genetic diversity and genetic differentiation of T. sebifera germplasm resources, 10 pairs of microsatellite markers were applied to 203 samples collected from eight populations. Forty-three alleles were detected. The average expected heterozygosity (He = 0.491) revealed a low level of genetic diversity. The genetic differentiation among T. sebifera populations was low (Fst = 0.026), which might be related to high gene flow (average Nm = 11.151). Genetic distance and structure results further confirmed that the genetic compositions of the eight populations were quite similar. One of the possible reasons for this phenomenon is that the early introduction and cultivation of T. sebifera were common, so gene exchange was frequent among populations. However, UPGMA clustering results indicated that the eight T. sebifera populations could still be divided into three categories. The classification was related to their geographical location: the southwestern group (ZY), central group (HG and XY) and eastern group (LS, HS, LX, XZ and LY). The reason for this differentiation might be severe deforestation following the decline in T. sebifera economic status. In addition, the central XY population had the largest number of rare alleles (4). In conclusion, although T. sebifera germplasm resources had a low level of genetic diversity, several rare alleles were detected in the central populations, which are valuable for breeding. These resources should be conserved to maintain genetic diversity in the T. sebifera populations. Moreover, geographical distances were important reasons for the limited genetic variations among the populations.