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

Red raspberry (Rubus idaeus 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 Rubus idaeus 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 Rubus idaeus 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.