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Article|10 May 2023|OPEN
Telomere-to-telomere carrot (Daucus carota) genome assembly reveals carotenoid characteristics
Ya-Hui Wang1 , Pei-Zhuo Liu1 , Hui Liu1 , Rong-Rong Zhang1 , Yi Liang4 , Zhi-Sheng Xu1 , Xiao-Jie Li4 , Qing Luo2 , Guo-Fei Tan2 , , Guang-Long Wang3 , and Ai-Sheng Xiong,1 ,
1State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
2Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou 550025, China
3School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu 223003, China
4Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops in North China, Beijing 100097, China
*Corresponding author. E-mail:,,

Horticulture Research 10,
Article number: uhad103 (2023)
Views: 134

Received: 03 Apr 2023
Accepted: 08 May 2023
Published online: 10 May 2023


Carrot (Daucus carota) is an Apiaceae plant with multi-colored fleshy roots that provides a model system for carotenoid research. In this study, we assembled a 430.40 Mb high-quality gapless genome to the telomere-to-telomere (T2T) level of “Kurodagosun” carrot. In total, 36 268 genes were identified and 34 961 of them were functionally annotated. The proportion of repeat sequences in the genome was 55.3%, mainly long terminal repeats. Depending on the coverage of the repeats, 14 telomeres and 9 centromeric regions on the chromosomes were predicted. A phylogenetic analysis showed that carrots evolved early in the family Apiaceae. Based on the T2T genome, we reconstructed the carotenoid metabolic pathway and identified the structural genes that regulate carotenoid biosynthesis. Among the 65 genes that were screened, 9 were newly identified. Additionally, some gene sequences overlapped with transposons, suggesting replication and functional differentiation of carotenoid-related genes during carrot evolution. Given that some gene copies were barely expressed during development, they might be functionally redundant. Comparison of 24 cytochrome P450 genes associated with carotenoid biosynthesis revealed the tandem or proximal duplication resulting in expansion of CYP gene family. These results provided molecular information for carrot carotenoid accumulation and contributed to a new genetic resource.