The draft genome of sweet orange (Citrus sinensis) has been sequenced and assembled, covering 87.3% of the estimated genome. The genome is relatively compact, with 20% composed of repetitive elements. A total of 29,445 protein-coding genes were predicted, half of which are heterozygous. Comparative analysis of seven citrus genomes suggests that sweet orange originated from a backcross hybrid between pummelo and mandarin. Analysis of genes involved in vitamin C metabolism revealed that GalUR, a key enzyme in the galacturonate pathway, is significantly upregulated in orange fruit, and the recent expansion of this gene family may provide a genomic basis for vitamin C production. The citrus genome is characterized by a high level of heterozygosity, with 50% of the genome showing heterozygosity. Genetic analysis using SSR and SNP markers supports the hypothesis that sweet orange originated from a hybrid between pummelo and mandarin, with a 1:3 ratio of genetic contributions from pummelo and mandarin. The genome also shows evidence of an ancient whole-genome duplication event, with no recent WGD events. The genome provides a valuable resource for understanding and improving citrus traits. The genome analysis revealed that citrus is closely related to cacao and Arabidopsis, and has a phylogenetic history dating back 85 million years. The genome also provides insights into the evolution of citrus, including the expansion of the GalUR gene family, which may be important for vitamin C accumulation in citrus fruits. The availability of the sweet orange genome sequence provides a valuable resource for citrus genetics and breeding improvement, and future studies may further enhance our understanding of citrus biology and evolution.The draft genome of sweet orange (Citrus sinensis) has been sequenced and assembled, covering 87.3% of the estimated genome. The genome is relatively compact, with 20% composed of repetitive elements. A total of 29,445 protein-coding genes were predicted, half of which are heterozygous. Comparative analysis of seven citrus genomes suggests that sweet orange originated from a backcross hybrid between pummelo and mandarin. Analysis of genes involved in vitamin C metabolism revealed that GalUR, a key enzyme in the galacturonate pathway, is significantly upregulated in orange fruit, and the recent expansion of this gene family may provide a genomic basis for vitamin C production. The citrus genome is characterized by a high level of heterozygosity, with 50% of the genome showing heterozygosity. Genetic analysis using SSR and SNP markers supports the hypothesis that sweet orange originated from a hybrid between pummelo and mandarin, with a 1:3 ratio of genetic contributions from pummelo and mandarin. The genome also shows evidence of an ancient whole-genome duplication event, with no recent WGD events. The genome provides a valuable resource for understanding and improving citrus traits. The genome analysis revealed that citrus is closely related to cacao and Arabidopsis, and has a phylogenetic history dating back 85 million years. The genome also provides insights into the evolution of citrus, including the expansion of the GalUR gene family, which may be important for vitamin C accumulation in citrus fruits. The availability of the sweet orange genome sequence provides a valuable resource for citrus genetics and breeding improvement, and future studies may further enhance our understanding of citrus biology and evolution.