Chromosome-Level Assembly of Flowering Cherry ( Prunus campanulata ) Provides Insight into Anthocyanin Accumulation

The flowering cherries (genus , subgenus ) are popular ornamental trees in China, Japan, Korea, and elsewhere. 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 cultivar "Lianmeiren", with only 0.54% of heterozygosity, as the focus of this study, and generated a high-quality chromosome-scale genome assembly of 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 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 genes from the genome. Based on the RNA-seq of five organs at three flowering stages, expression analyses revealed that the majority of the 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 and .