Haplotype-resolved genome of a papeda provides insights into the geographical origin and evolution of Citrus.

The publication of several high-quality genomes has contributed greatly to clarifying the evolution of citrus. However, due to their complex genetic backgrounds, the origins and evolution of many citrus species remain unclear. We assembled de novo the 294-Mbp chromosome-level genome of a more than 200-year-old primitive papeda (DYC002). Comparison between the two sets of homologous chromosomes of the haplotype-resolved genome revealed 1.2% intragenomic variations, including 1.75 million SNPs, 149,471 insertions and 154,215 deletions. Using this genome as a reference, we resequenced and performed population and phylogenetic analyses of 378 representative citrus accessions. Our study confirmed that the primary origin center of core Citrus species is in South China, particularly in the Himalaya-Hengduan Mountains. Papeda species are an ancient Citrus type compared with C. ichangensis. We found that the evolution of the Citrus genus followed two radiations through two routes (to East China and Southeast Asia) along river systems. Evidence for the origin and evolution of some individual citrus species was provided. Papeda probably played an important role in the origins of Australian finger lime, citrons, Honghe papeda and pummelos; Ichang papeda originated from Yuanjiang city of Yunnan Province, China, and C. mangshanensis has a close relationship with kumquat and Ichang papeda. Moreover, the Hunan and Guangdong Provinces of China are predicted to be the origin center of mandarin, sweet orange and sour orange. Additionally, our study revealed that fruit bitterness was significantly selected against during citrus domestication. Taken together, this study provides new insight into the origin and evolution of citrus species and may serve as a valuable genomic resource for citrus breeding and improvement.