The High-Quality Genome Sequencing and Analysis of Red Raspberry ( Rubus idaeus L.)

Red raspberry ( L.), which is an important nutritional source for human health, belongs to fruit crops of the Rosaceae family. Here, we used Pacific Biosciences single-molecule real-time (SMRT) sequencing and high-throughput chromosome conformation capture (Hi-C) sequencing technologies to assemble genomes and reported a high-quality L. (DNS-1) genome with 321.29 Mb assembled into seven chromosomes. The LAI score of the DNS-1 genome assembly was 21.32, belonging to gold quality. Approximately 52.3% of the assembly sequences were annotated as repetitive sequences, and 24.15% were composed of long terminal repeat elements. A total of 29,814 protein-coding genes and 2474 pseudogenes were predicted in DNS-1. We characterized the complete genomes of DNS-1 and compared them to those of seven other species. We found that 652 gene families were unique to DNS-1 and they were shaped from an ancestor. There were 1000 and 5193 gene families that expanded and contracted in the DNS-1 genome. The L. genome can be used to understand the structure and evolution of Rosaceae genomes and can be developed to identify genes controlling important traits and improve breeding work.