Assembling the chromosome-level genome of Arctium Lappa L. provides new insights into carotenoid biosynthesis.

BACKGROUND: Arctium lappa L. (A. lappa), a plant of significant economic importance, is cultivated worldwide for its applications in food and medicine, presenting a compelling opportunity for genetic research within the Asteraceae family. Despite the importance of A. lappa genetic resources, the genome of the Peixian yellow A. lappa cultivar has not yet been sequenced. RESULTS: This study presents a chromosome-level genome of the Peixian yellow A. lappa, the genome consists of a comprehensive 1.69 Gb reference and a scaffold N50 of 91.02 Mb. By utilizing Hi-C data, we anchored 99.12% of the assembled sequences onto 18 chromosomes and identified 40,665 protein-coding genes. The genome is predominantly composed of repetitive sequences, which constitute 68.32%, with long terminal repeats (LTRs) accounting for 65.66% of the total. A comparative genomic analysis with the Gansu A. lappa genome revealed significant genetic variations, including 2,972,809 single nucleotide polymorphisms (SNPs), 608,644 insertions/deletions (INDELs), and 11,800 structural variations (SVs). Furthermore, transcriptomic analyses comparing Peixian yellow A. lappa and Liu chuan li xiang A. lappa have shed light on the molecular mechanisms underlying carotenoid biosynthesis in Peixian yellow A. lappa. A total of 16 differentially expressed genes (DEGs) were specifically associated with the carotenoid biosynthesis pathway. Among these, several genes, including PSY1, PDS, BCH2, VDE, NCED1, and NCED2, were downregulated in Peixian yellow A. lappa. In contrast, other genes such as DXS, IDI1, CCD8B, CCS, and CCD4 were upregulated. Additionally, several transcription factors linked to carotenoid biosynthesis were identified, including MYC2, WRK35, and HY5. Most of these transcription factors were downregulated in Peixian yellow A. lappa, with the exception of Arcla.08g00830, which encodes MYC2. CONCLUSION: This high-quality genomic resource is poised to enhance genome-informed breeding strategies and improve A. lappa quality, offering valuable insights for breeding programs aimed at enhancing desirable traits in A. lappa.