Analysis of telomere-to-telomere genome of red carrot TXH4 elucidates the role of DcLCYE and DcLCYB1 in lycopene accumulation in carrot.

Carrot taproots exhibit a wide range of colors due to variations in carotenoid and anthocyanin contents. TouXinHong4 (TXH4), a Chinese red carrot landrace from western China, is appreciated for its storability, stress tolerance, and good flavor. In this study, we generated a high-quality, telomere-to-telomere (T2T), gap-free genome assembly of TXH4, with a total size of 449.92 Mb. Repetitive sequences accounted for 48.6% of the genome. A total of 34 225 genes were identified, with 34 016 genes associated with at least one functional annotation. Comparison with two previously assembled carrot genomes, Daucus carota T2T (DcT2T) and D. carota v2.0 (DcRef), revealed 2 466 422 and 2 037 986 single nucleotide polymorphisms and 500 579 and 474 704 insertions/deletions in DcT2T and DcRef, respectively. Carotenoid analysis showed that the lycopene content in TXH4 roots was 1965-fold higher than that in the leaves, while α-carotene and β-carotene levels in the roots were only 2.7% and 3.5% of those in the leaves, respectively. This finding was consistent with the lack of transcription of lycopene β-cyclase 1 (LCYB1) and lycopene ε-cyclase (LCYE) in TXH4 roots. Furthermore, overexpression of DcLCYB1 and DcLCYE resulted in reduced lycopene levels, while their knockout led to elevated lycopene accumulation. Downregulation of DcLCYB1 and DcLCYE was identified as a critical factor contributing to lycopene accumulation, resulting in the red root phenotype of TXH4 roots. The gapless genome assembly of TXH4 offers important insights into the red carrot genome and expands the genomic resources for breeding, facilitating more efficient genome-assisted breeding strategies for crop improvement.