Viburnum japonicum (Thunb.) Sprengel is an endangered species endemic to coastal regions of eastern Asia (China, Japan, and South Korea). However, its systematic position has been controversial. In this study, we present the complete chloroplast (cp) genome of V. japonicum (GenBank OP644292) sequenced using the Illumina NovaSeq platform. The cp genome has a total length of 158,606 bp and a G+C contents of 38.08%. It consists of a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeats (IRs) regions measuring 87,060 bp, 18,510 bp, and 26,516 bp, respectively. A total of 131 genes were identified, including 87 protein-coding genes, 36 transfer RNA genes (tRNAs), and 8 ribosomal RNA genes(rRNAs). Additionally, a total of 44 dispersed repeats were detected, including three types: forward, palindromic, and reverse. Among the 38 SSR loci that were discovered, the majority were mononucleotide loci composed of A/T. Furthermore, we found that 15 genes (accD, atpF, ndhA, ndhB, petB, petD, rpl16, rpl2, rpoC1, rps12, rps16, trnA-UGC, trnI, trnK-UUU, and trnL-UAA) contain one intron, while clpP and ycf3 have two introns. The relative synonymous codon usage (RSCU) analysis detected 31 high-frequency codons, where A/U bases accounted for 93.55% of the total, indicating an asymmetry in chloroplast gene and a presence for A/U bases. Comparative analysis of genome structure and sequences data of V. japonicum chloroplast genomes in comparison with other closely related species demonstrated a high level of conservation in their structure and organization. Furthermore, three mutation hotspots (psbH, rps19, and trnL) were identified, which could be valuable for future phylogenetic and population genetic research. Phylogenetic analysis revealed that the two accessions of V. japonicum are closely related to a group of V. setigerum, V. erosum, and V. fordiae within the Viburnum genus. In conclusion, this study provides important insights for accurately identifying and understanding the phylogeny of Viburnum species through the complete cp genome sequencing of V. japonicum.

Cerasus serrulata (Rosaceae) is an important flowering cherry resource which is valuable for developing new cultivars of flowering cherries. It is broadly distributed and possesses abundant variations. In this study, phylogeographic analysis was conducted to reveal the evolutionary history to better understand the genetic diversity and genetic structure of C. serrulata so as to provide more accurate molecular insights into better conservation and utilization of the germplasm resources. A total of 327 individuals from 18 wild populations were collected. Three chloroplast DNA (cpDNA) fragments (matK, trnD‐E, and trnS‐G) and the nuclear internal transcribed spacer (ITS) were utilized. The results showed a high genetic diversity at both species level and population level of C. serrulata. High genetic differentiation and the existence of the phylogeographic structure were detected. No significant expansion events were discovered. Two geographic lineages were inferred. One was confined to the Qinling Mountains and the Taihang Mountains. The other was from the Wuling Mountains to the Jiangnan Hilly Regions and then went northeast to the coast of Asia. In addition, some taxonomic treatments of the C. serrulata complex are discussed and reconsidered. Conservation and utilization strategies of wild C. serrulata germplasm resources were recommended.

Cerasus dielsiana (Rosaceae) is one of the most characteristic wild flowering cherry species endemic to subtropical China, with high conservation value from ornamental, economic, and ecological perspectives. To verify its spatial genetic structure and phylogeographic history, evaluation of nuclear (ITS) sequence variation in 203 individuals from 25 wild populations across its natural distribution ranges was conducted. High levels of ribotypes and nuclear diversity (H_d = 0.879 ± 0.012, π = 3.56 ± 0.16) were detected at the species level. Spatial analysis of molecular variation (SAMOVA), median-joining network and phylogenetic Neighbour-joining tree assigned the populations into four genetically distinct groups. Meanwhile, high levels of genetic differentiation among populations and strong phylogeographic patterns (N_st = 0.837 > G_st = 0.585; P < 0.05) were revealed based on the analysis of molecular variance (AMOVA). Results of neutrality tests, mismatch distribution analyses, Mantel test, barrier analyses, together with ecological niche modelling (ENM) simulation and BEAST analysis suggest a long-term demographic history (95% HPD: 3.64–8.83 Mya) of C. dielsiana, and at least three potential in situ glacial refugia as well as recent demographic expansion in eastern region have been detected. Collectively, we highlight that the combined effect of natural selection and random genetic drift under complex topography and palaeoclimatic oscillations since the Last Glacial Maximum (LGM) in subtropical China might have been the main driver to the species’ allopatric differentiation. Scientific conservation and sustainable utilization for wild C. dielsiana germplasm resources were subsequently proposed.