Chromosome-scale genome assembly of Prunus pusilliflora provides novel insights into genome evolution, disease resistance, and dormancy release in Cerasus L

Chromosome-level genome assembly provides insights into the genetic diversity, evolution, and flower development of Prunus conradinae

Prunus conradinae, a valuable flowering cherry belonging to the Rosaceae family subgenus Cerasus and endemic to China, has high economic and ornamental value. However, a high-quality P. conradinae genome is unavailable, which hinders our understanding of its genetic relationships and phylogenesis, and ultimately, the possibility of mining of key genes for important traits. Herein, we have successfully assembled a chromosome-scale P. conradinae genome, identifying 31,134 protein-coding genes, with 98.22% of them functionally annotated. Furthermore, we determined that repetitive sequences constitute 46.23% of the genome. Structural variation detection revealed some syntenic regions, inversions, translocations, and duplications, highlighting the genetic diversity and complexity of Cerasus. Phylogenetic analysis demonstrated that P. conradinae is most closely related to P. campanulata, from which it diverged ~ 19.1 million years ago (Mya). P. avium diverged earlier than P. cerasus and P. conradinae. Similar to the other Prunus species, P. conradinae underwent a common whole-genome duplication event at ~ 138.60 Mya. Furthermore, 79 MADS-box members were identified in P. conradinae, accompanied by the expansion of the SHORT VEGETATIVE PHASE subfamily. Our findings shed light on the complex genetic relationships, and genome evolution of P. conradinae and will facilitate research on the molecular breeding and functions of key genes related to important horticultural and economic characteristics of subgenus Cerasus.

Occurrence and Characterization of Sclerotinia sclerotiorum Causing Fruit Rot on Sweet Cherry in Southern China

Sweet cherry (Prunus avium L.) is widely planted in northern China due to its high economic value, and its cultivation has gradually spread south to warm regions. However, fruit rot, observed on the young fruits, poses a considerable threat to the development of sweet cherry. To determine the causal agent, morphological observation, molecular identification, and pathogenicity tests were performed on isolates obtained from diseased fruits. As a result, Sclerotinia sclerotiorum was identified as the pathogen. Pathogenicity tests on different sweet cherry cultivars indicated that 'Summit' was highly sensitive to S. sclerotiorum, whereas 'Hongmi' showed significant resistance. Besides sweet cherry, S. sclerotiorum could also infect other vegetable crops we tested, such as cowpea, soybean, tomato, and chili. Fungicide sensitivity and efficacy assays showed that both fludioxonil and pyraclostrobin can effectively inhibit the mycelial growth of S. sclerotiorum and decrease disease incidences on the young fruits of sweet cherry. Furthermore, genome sequencing resulted in a 37.8 Mb assembly of S. sclerotiorum strain ScSs1, showing abundant SNPs, InDels, and SVs with the genome of S. sclerotiorum reference strain 1980 UF-70. The above results provide an important basis for controlling the fruit rot of sweet cherry caused by S. sclerotiorum in China.