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.

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.

Background: Prunus campanulata, a species of ornamental cherry, holds significant genetic and horticultural value. Despite the availability of various cherry genomes, a fully resolved telomere-to-telomere (T2T) assembly for this species has been lacking. Recent advancements in long-read sequencing technologies have made it possible to generate gap-free genome assemblies, providing comprehensive insights into genomic structures that were previously inaccessible. Findings: We present the first T2T genome assembly for P. campanulata “Lianmeiren” (v2.0), achieved through the integration of PacBio HiFi, ultra-long Oxford Nanopore Technologies, Illumina, and Hi-C sequencing. The assembly resulted in a highly contiguous genome with a total size of 266.23 Mb and a contig N50 of 31.6 Mb. The genome exhibits remarkable completeness (98.9% BUSCO) and high accuracy (quality value of 48.75). Additionally, 13 telomeres and putative centromere regions were successfully identified across the 8 pseudochromosomes. Comparative analysis with the previous v1.0 assembly revealed 336,943 single nucleotide polymorphisms, 107,521 indels, and 1,413 structural variations, along with the annotation of 1,402 new genes. Conclusions: This T2T genome assembly of P. campanulata “Lianmeiren” provides a critical reference for understanding the genetic architecture of the species. It enhances our ability to study structural variations, gene function, and evolutionary biology within the Prunus genus.

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.

"Prunus conradinae ‘Luoshifener’, a Flowering Cherry Cultivar with a Strong Aroma" published on Nov 2022 by American Society for Horticultural Science.