Dataset Information

The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis

ABSTRACT:

BACKGROUND: Traditional Chinese medicine has used Peucedanum praeruptorum Dunn (Apiaceae) for a long time. Various coumarins, including the significant root constituents Praeruptorin (A-E), are the active constituents of the dried roots of P. praeruptorum. Previous transcriptomic and metabolomic studies attempted to elucidate the distribution and biosynthetic network of these medicinal-valuable compounds. However, the lack of a high-quality reference genome impedes an in-depth understanding of genetic traits and, thus, the development of better breeding strategies.

RESULTS: The authors assembled a telomere-to-telomere genome by combining PacBio HiFi, ONT ultra- long and Hi-C data. The final genome assembly was approximately 1.798 Gb, assigned to 11 chromosomes and genome completeness >98%. Comparative genomic analysis suggested that P. praeruptorum experienced two WGD events like the ones in the Apiaceae family. By the transcriptomic and metabolomic analysis of the coumarin metabolic pathway, we presented coumarins' spatial and temporal distribution and the expression patterns of critical genes for its biosynthesis. Notably, the COSY and cytochrome P450 genes showed tandem duplications on several chromosomes, which may be responsible for the high accumulation of coumarins.

CONCLUSIONS: The authors obtained a T2T genome for P. praeruptorum, which provides molecular insights into the chromosomal distribution of the coumarin biosynthetic genes. This high-quality genome is an essential resource for designing engineering strategies for improving the production of these valuable compounds.

INSTRUMENT(S): Liquid Chromatography MS - negative - reverse phase, Liquid Chromatography MS - positive - reverse phase

PROVIDER: MTBLS8679 | MetaboLights | 2024-04-02

REPOSITORIES: MetaboLights

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			Action	DRS
	22P2248000101_OCTML_NEG.raw	Raw
	22P22480001_OCTML_NEG.raw	Raw
	22P2248000201_OCTML_NEG.raw	Raw
	22P22480002_OCTML_NEG.raw	Raw
	22P2248000301_OCTML_NEG.raw	Raw

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The telomere-to-telomere (T2T) genome of Peucedanum praeruptorum Dunn provides insights into the genome evolution and coumarin biosynthesis.

Bai Mingzhou M Jiang Sanjie S Chu Shanshan S Yu Yangyang Y Shan Dai D Liu Chun C Zong Liang L Liu Qun Q Liu Nana N Xu Weisong W Mei Zhanlong Z Jian Jianbo J Zhang Chi C Zhao Shancen S Chiu Tsan-Yu TY Simonsen Henrik Toft HT

GigaScience 20240101

<h4>Background</h4>Traditional Chinese medicine has used Peucedanum praeruptorum Dunn (Apiaceae) for a long time. Various coumarins, including the significant constituents praeruptorin (A-E), are the active constituents in the dried roots of P. praeruptorum. Previous transcriptomic and metabolomic studies have attempted to elucidate the distribution and biosynthetic network of these medicinal-valuable compounds. However, the lack of a high-quality reference genome impedes an in-depth understandi ...[more]

PMID: 38837945

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