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Telomere-to-telomere carrot (Daucus carota) genome assembly reveals carotenoid characteristics

文献类型： 外文期刊

作者： Wang, Ya-Hui 1 ; Liu, Pei-Zhuo 1 ; Liu, Hui 1 ; Zhang, Rong-Rong 1 ; Liang, Yi 4 ; Xu, Zhi-Sheng 1 ; Li, Xiao-Jie 4 ; Luo, Qing 2 ; Tan, Guo-Fei 2 ; Wang, Guang-Long 3 ; Xiong, Ai-Sheng 1 ;

作者机构： 1.Nanjing Agr Univ, Coll Hort, State Key Lab Crop Genet & Germplasm Enhancement &, Minist Agr & Rural Affairs,Key Lab Biol & Germplas, Nanjing 210095, Jiangsu, Peoples R China

2.Guizhou Acad Agr Sci, Inst Hort, Guiyang 550025, Guizhou, Peoples R China

3.Huaiyin Inst Technol, Sch Life Sci & Food Engn, Huaian 223003, Jiangsu, Peoples R China

4.Beijing Acad Agr & Forestry Sci, Beijing Vegetable Res Ctr, Key Lab Biol & Genet Improvement Hort Crops North, Beijing 100097, Peoples R China

期刊名称：HORTICULTURE RESEARCH （ 影响因子：8.7； 五年影响因子：9.0 ）

ISSN： 2662-6810

年卷期： 2023 年 10 卷 7 期

页码：

收录情况： SCI

摘要： 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.

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