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

Abstract

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.

Acknowledgements

This article was supported by National Natural Science Foundation of China (32072563, 32102369), Natural Science Foundation of Jiangsu Province (BK20211366), Project of Guizhou Provincial Department of Science and Technology (Qiankehe Fuqi [2022 005]), and Project of Guiyang of Science and Technology Bureau (Zhuke contract [2021]5-1), Priority Academic Program Development of Jiangsu Higher Education Institutions Project (PAPD).

Author contributions

Y.H.W. and A.S.X initiated and designed the research. Y.H.W., P.Z.L., R.R.Z, X.J.L., and Q.L. performed the experiments. Y.H.W., H.L., and Z.S.X. analyzed the data. Y.L., G.L.W., G.F.T., and A.S.X. contributed the reagents/materials/analysis tools. Y.H.W. wrote the paper. A.S.X., G.F.T., and G.L.W. were involved in finalizing the manuscript.

Data availability

The genome raw sequencing (including ONT Ultra-long, PacBio HiFi, Hi-C, and next-generation), assembly, and annotation data are accessible in the NCBI (https://www.ncbi.nlm.nih.gov/) database with the BioProject accession number PRJNA967095.

Conflict of interest statement

The authors report no conflict of interest.

Supplementary data

Supplementary data is available at Horticulture Research online.

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