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.

Prunus speciosa (Oshima cherry) is a flowering tree species with high ornamental and economic values and is also an indigenous species with a very limited natural distribution in Japan. Here we determined the first complete chloroplast genome of P. speciosa using genome skimming approach. The cp genome was 157,916 bp long, with a large single-copy region (LSC) of 85,927 bp and a small single-copy region (SSC) of 19,123 bp separated by a pair of inverted repeats (IRs) of 26,433 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and eight ribosomal RNA genes. The phylogenetic analysis indicated that P. speciosa is close related with ‘P. serrulata var. spontanea’ auct. non. (P. leveilleana).

The flowering cherries (genus Prunus, subgenus Cerasus) are popular ornamental trees in China, Japan, Korea, and elsewhere. Prunus campanulata Maxim. is an important species of flowering cherry native to Southern China, which is also distributed in Taiwan, the Ryukyu Islands of Japan, and Vietnam. It produces bell-shaped flowers with colors ranging from bright pink to crimson during the Chinese Spring Festival from January to March each year. We selected the P. campanulata cultivar “Lianmeiren”, with only 0.54% of heterozygosity, as the focus of this study, and generated a high-quality chromosome-scale genome assembly of P. campanulata by combining Pacific Biosciences (PacBio) single-molecule sequencing, 10× Genomics sequencing, and high-throughput chromosome conformation capture (Hi-C) technology. We first assembled a 300.48 Mb genome assembly with a contig N50 length of 2.02 Mb. In total, 28,319 protein-coding genes were predicted from the genome, 95.8% of which were functionally annotated. Phylogenetic analyses indicated that P. campanulata diverged from a common ancestor of cherry approximately 15.1 million years ago. Comparative genomic analyses showed that the expanded gene families were significantly involved in ribosome biogenesis, diterpenoid biosynthesis, flavonoid biosynthesis, and circadian rhythm. Furthermore, we identified 171 MYB genes from the P. campanulata genome. Based on the RNA-seq of five organs at three flowering stages, expression analyses revealed that the majority of the MYB genes exhibited tissue-specific expression patterns, and some genes were identified as being associated with anthocyanin accumulation. This reference sequence is an important resource for further studies of floral morphology and phenology, and comparative genomics of the subgenera Cerasus and Prunus.

Introduction: Tetrastigma hemsleyanum is a folk and rare medicinal plant, and specifically, it is distributed in the south, China. To investigate the cumulative properties of its medicinal components, we examined the effect of UV light on flavonoid content and related enzyme activity changes in T. hemsleyanum.Methods: The leaves and tubers were treated with UV-A, UV-B and UV-C for 1 h, 1L/23D h, 3 h and 3L/21D h (D represents darkness treatment). High-performance liquid chromatography (HPLC) analysis showed that the content of many flavonoids decreased significantly during UV-A treatment, increased after UV-B and UV-C irradiation and accumulated again after darkness treatment.Results: In the root tubers of the UV-A group, naringin content in the 3L/21D h group (0.069 μg/g) was 16.30 times higher than that of 3 h group (0.0042 μg/g). The rutin content was elevated after UV irradiation but was not detected in the CK group. The test results of the enzyme-linked kit indicated that the activities of many enzymes were higher in the UV-A and UV-B irradiation groups than those in the CK group, but the results were reversed in the UV-C treatment. After darkness treatment, the activities of most enzymes were higher than those with UV irradiation alone; F3’5’H activity in the 3L/21D h group (97.25 U/L) was 1.24 times higher than that in the 3 h group (78.12 U/L) in the UV-A-treated group.Discussion: The study results suggest that appropriate UV-B and UV-C irradiation, as well as darkness supplementation, had a promotive effect on flavonoids in the leaves and root tubers of T. hemsleyanum. Additionally, UV irradiation and darkness treatment enhanced the activity of most enzymes.

Prunus matuurai is an endemic flowering cherry on Taiwan Island, China. Here, we determined the first complete chloroplast genome of P. matuurai using genome skimming approach. The cp genome was 157,928 bp long, with a large single-copy region (LSC) of 85,904 bp and a small single-copy region (SSC) of 19,104 bp separated by a pair of inverted repeats (IRs) of 26,460 bp. It encodes 129 genes, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. The phylogenetic analysis indicated that P. matuurai is closely related to P. speciose.